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1 <tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.1">
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2 <description>uses the output from computeGCBias to generate corrected BAM files</description>
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3 <expand macro="requirements" />
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4 <macros>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <command>
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8 #import tempfile
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9 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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10
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11 #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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12 #set $temp_bam_path = $temp_bam_handle.name + '.bam'
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13 #silent $temp_bam_handle.close()
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14 #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
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15 #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
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16
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17
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18 correctGCBias
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19
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20 @THREADS@
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21
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22 --bamfile '$temp_bam_path'
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23 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
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24
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25 @reference_genome_source@
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26
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27
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28 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
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29 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
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30 #else:
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31 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
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32 #end if
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33
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34
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35 #if $advancedOpt.showAdvancedOpt == "yes":
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36 #if str($advancedOpt.region.value) != '':
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37 --region '$advancedOpt.region'
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38 #end if
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39
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40 --binSize '$advancedOpt.binSize'
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41 #end if
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42
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43 #set newoutFileName="corrected."+str($outFileFormat)
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44
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45 --correctedFile $newoutFileName; mv $newoutFileName $outFileName
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46
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47 </command>
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48
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49 <inputs>
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50
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51 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
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52
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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."/>
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54
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55 <expand macro="reference_genome_source" />
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56 <expand macro="effectiveGenomeSize" />
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57
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58 <param name="outFileFormat" type="select" label="File format of the output">
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59 <option value="bam">bam</option>
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60 <option value="bw">bigwig</option>
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61 <option value="bg">bedgraph</option>
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62 </param>
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63
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64 <conditional name="advancedOpt">
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65 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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66 <option value="no" selected="true">no</option>
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67 <option value="yes">yes</option>
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68 </param>
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69 <when value="no" />
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70 <when value="yes">
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71 <param name="region" type="text" value=""
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72 label="Region of the genome to limit the operation to"
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73 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" />
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74
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75 <param name="binSize" type="integer" value="50" min="1"
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76 label="Bin size in bp"
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77 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
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78 </when>
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79 </conditional>
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80 </inputs>
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81
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82 <outputs>
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83 <data format="bam" name="outFileName">
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84 <change_format>
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85 <when input="outFileFormat" value="bw" format="bigwig" />
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86 <when input="outFileFormat" value="bam" format="bam" />
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87 <when input="outFileFormat" value="bg" format="bedgraph" />
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88 </change_format>
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89 </data>
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90 </outputs>
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91 <help>
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92
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93 **What it does**
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94
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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.
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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.
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97
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98 **Output files**:
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99
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100 - GC-normalized BAM file
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101
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102 -----
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103
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104 .. class:: infomark
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105
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106 @REFERENCES@
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107
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108 </help>
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109 </tool>
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