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1 <tool id="correctGCBias" name="correctGCBias" version="1.0">
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2 <description>
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3 </description>
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4 <command>
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5 correctGCBias
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6 --bamfile '$bamInput'
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7 --species '$species'
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8 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
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9
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10 #if $source.ref_source=="history":
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11 --genome $source.input1
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12 #else:
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13 --genome "${source.input1_2bit.fields.path}"
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14 #end if
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15
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16 #if $advancedOpt.showAdvancedOpt == "yes":
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17 #if str($advancedOpt.region.value) != '':
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18 --region '$advancedOpt.region'
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19 #end if
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20
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21 --binSize '$advancedOpt.binSize'
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22 #end if
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23
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24 #set newoutFileName="corrected."+str($outFileFormat)
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25
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26 --correctedFile $newoutFileName; mv $newoutFileName $outFileName
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27
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28 </command>
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29
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30 <inputs>
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31
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32 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
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33
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34 <param name="bamInput" format="bam" type="data" label="Input BAM file" help="The BAM file must be sorted and indexed."/>
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35
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36 <param name="species" type="text" value="" label="Species name abbreviation" />
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37
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38 <conditional name="source">
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39 <param name="ref_source" type="select" label="Reference genome">
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40 <option value="cached">locally cached</option>
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41 <option value="history">in your history</option>
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42 </param>
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43 <when value="cached">
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44 <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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45 <options from_data_table="lastz_seqs" />
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46 </param>
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47 </when>
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48 <when value="history">
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49 <param name="input1" type="data" format="bam" label="Select a reference dataset in 2bit format" />
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50 </when>
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51 </conditional>
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52
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53 <param name="outFileFormat" type="select" label="File format of the output">
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54 <option value="bam">bam</option>
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55 <option value="bw">bigwig</option>
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56 <option value="bg">bedgraph</option>
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57 </param>
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58
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59 <conditional name="advancedOpt">
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60 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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61 <option value="no" selected="true">no</option>
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62 <option value="yes">yes</option>
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63 </param>
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64 <when value="no" />
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65 <when value="yes">
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66 <param name="region" type="text" value=""
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67 label="Region of the genome to limit the operation to"
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68 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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69
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70 <param name="binSize" type="integer" value="50" min="1"
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71 label="Bin size in bp"
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72 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
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73 </when>
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74 </conditional>
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75 </inputs>
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76
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77 <outputs>
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78 <data format="bam" name="outFileName">
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79 <change_format>
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80 <when input="outFileFormat" value="bw" format="bigwig" />
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81 <when input="outFileFormat" value="bam" format="bam" />
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82 <when input="outFileFormat" value="bg" format="bedgraph" />
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83 </change_format>
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84 </data>
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85 </outputs>
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86 <help>
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87
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88 **What it does**
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89
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90 Computes the GC bias ussing Benjamini's method [citation]. The resulting GC
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91 bias can later be used to plot the bias or to correct the bias.
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92
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93 -----
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94
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95 .. class:: infomark
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96
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97 Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_.
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98
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99 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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100
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101
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102 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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103 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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104 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
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105
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106 </help>
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107
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108 </tool>
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