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1 <tool id="deeptools_correctGCBias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
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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 <expand macro="stdio" />
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5 <macros>
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6 <token name="@BINARY@">correctGCBias</token>
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7 <import>deepTools_macros.xml</import>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11 ln -s $bamInput local_bamInput.bam;
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12 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
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13
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14 correctGCBias
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15 @THREADS@
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16 --bamfile local_bamInput.bam
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17 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
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18
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19 @reference_genome_source@
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20
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21 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
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22 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
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23 #else:
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24 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
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25 #end if
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26
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27 #if str($region).strip() != '':
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28 --region '$region'
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29 #end if
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30 --correctedFile $outFileName
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31 ]]>
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32 </command>
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33 <inputs>
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34 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
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35 <param name="bamInput" format="bam" type="data"
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36 label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
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37 <expand macro="reference_genome_source" />
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38 <expand macro="effectiveGenomeSize" />
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39 <expand macro="region_limit_operation" />
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40 </inputs>
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41 <outputs>
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42 <data format="bam" name="outFileName" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
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47 <param name="bamInput" value="phiX.bam" ftype="bam" />
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48 <param name="ref_source" value="history" />
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49 <param name="input1" value="phiX.2bit" />
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50 <param name="effectiveGenomeSize_opt" value="specific" />
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51 <param name="effectiveGenomeSize" value="5386" />
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52 <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" compare="sim_size" />
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53 </test>
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54 </tests>
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55 <help>
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56 <![CDATA[
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57 **What it does**
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58
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59 This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by
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60 Benjamini and Speed (2012) Nucleic Acids Res.
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61 The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.
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62
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63 You can find more details on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
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64
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65
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66 **Output files**:
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67
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68 - GC-normalized BAM file
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69
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70 -----
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71
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72 @REFERENCES@
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73 ]]>
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74 </help>
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75 <expand macro="citations" />
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76 </tool>
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