Mercurial > repos > bgruening > deeptools

annotate correctGCBias.xml @ 30:5231f398d784 draft

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author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
parents 3a2aab18a217
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f7712a057440 new bugfix release
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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 <macros>
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4 <token name="@BINARY@">correctGCBias</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 <![CDATA[
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10 ln -s $bamInput local_bamInput.bam;
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11 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
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13 correctGCBias
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14 @THREADS@
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15 --bamfile local_bamInput.bam
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16 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
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18 @reference_genome_source@
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20 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
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21 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
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22 #else:
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23 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
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24 #end if
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26 #if str($region).strip() != '':
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27 --region '$region'
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28 #end if
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29 --correctedFile corrected.bam;
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31 mv corrected.bam $outFileName;
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32 ]]>
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33 </command>
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34 <inputs>
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35 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
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36 <param name="bamInput" format="bam" type="data"
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37 label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted. (--bamfile)" />
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38 <expand macro="reference_genome_source" />
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39 <expand macro="effectiveGenomeSize" />
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40 <expand macro="region_limit_operation" />
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41 </inputs>
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42 <outputs>
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43 <data format="bam" name="outFileName" />
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
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48 <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
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49 <param name="ref_source" value="history" />
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50 <param name="input1" value="sequence.2bit" />
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51 <param name="effectiveGenomeSize_opt" value="specific" />
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52 <param name="effectiveGenomeSize" value="23011544" />
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53 <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" />
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54 </test>
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55 </tests>
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56 <help>
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57 <![CDATA[
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58 **What it does**
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60 This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by
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61 Benjamini and Speed (2012) Nucleic Acids Res.
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62 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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64 You can find more details on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
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67 **Output files**:
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69 - GC-normalized BAM file
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71 -----
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73 @REFERENCES@
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74 ]]>
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75 </help>
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76 <expand macro="citations" />
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77 </tool>