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1 <tool id="correctGCBias" name="correctGCBias" version="1.0.1">
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2 <description>use the output from computeGCBias to obtain corrected sample files</description>
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3 <requirements>
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4 <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
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5 <requirement type="package" version="0.1">ucsc_tools</requirement>
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6 </requirements>
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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), $temp_bam_path))
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16
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17
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18 correctGCBias
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19 --bamfile '$temp_bam_path'
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20 --species '$species'
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21 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
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22
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23 #if $source.ref_source=="history":
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24 --genome $source.input1
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25 #else:
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26 --genome "${source.input1_2bit.fields.path}"
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27 #end if
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28
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29 #if $advancedOpt.showAdvancedOpt == "yes":
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30 #if str($advancedOpt.region.value) != '':
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31 --region '$advancedOpt.region'
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32 #end if
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33
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34 --binSize '$advancedOpt.binSize'
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35 #end if
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36
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37 #set newoutFileName="corrected."+str($outFileFormat)
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38
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39 --correctedFile $newoutFileName; mv $newoutFileName $outFileName
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40
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41 </command>
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42
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43 <inputs>
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44
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45 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
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46
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47 <param name="bamInput" format="bam" type="data" label="Input BAM file" help="The BAM file must be sorted and indexed."/>
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48
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49 <param name="species" type="select" label="Species name abbreviation">
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50 <option value="hg19">hg19</option>
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51 <option value="ce10">ce10</option>
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52 <option value="dm3">dm3</option>
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53 <option value="mm9">mm9</option>
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54 </param>
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55
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56 <conditional name="source">
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57 <param name="ref_source" type="select" label="Reference genome">
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58 <option value="cached">locally cached</option>
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59 <option value="history">in your history</option>
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60 </param>
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61 <when value="cached">
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62 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact your Galaxy team">
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63 <options from_data_table="deepTools_seqs" />
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64 </param>
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65 </when>
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66 <when value="history">
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67 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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68 </when>
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69 </conditional>
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70
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71 <param name="outFileFormat" type="select" label="File format of the output">
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72 <option value="bam">bam</option>
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73 <option value="bw">bigwig</option>
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74 <option value="bg">bedgraph</option>
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75 </param>
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76
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77 <conditional name="advancedOpt">
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78 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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79 <option value="no" selected="true">no</option>
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80 <option value="yes">yes</option>
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81 </param>
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82 <when value="no" />
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83 <when value="yes">
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84 <param name="region" type="text" value=""
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85 label="Region of the genome to limit the operation to"
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86 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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87
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88 <param name="binSize" type="integer" value="50" min="1"
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89 label="Bin size in bp"
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90 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
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91 </when>
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92 </conditional>
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93 </inputs>
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94
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95 <outputs>
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96 <data format="bam" name="outFileName">
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97 <change_format>
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98 <when input="outFileFormat" value="bw" format="bigwig" />
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99 <when input="outFileFormat" value="bam" format="bam" />
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100 <when input="outFileFormat" value="bg" format="bedgraph" />
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101 </change_format>
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102 </data>
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103 </outputs>
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104 <help>
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105
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106 **What it does**
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107
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108 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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109 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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110 -----
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111
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112 .. class:: infomark
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113
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114 If you would like to give us feedback or you run into any trouble, please sent an email to deeptools@googlegroups.com
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115
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116 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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117
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118
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119 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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120 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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121 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
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122
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123 </help>
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124
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125 </tool>
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