Mercurial > repos > bgruening > deeptools_correct_gc_bias

annotate correctGCBias.xml @ 0:748076af9837 draft

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author bgruening
date Mon, 25 Jan 2016 20:23:49 -0500
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children 4930eb430843
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1 <tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
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2 <description>uses the output from computeGCBias to generate GC-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 @BINARY@
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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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19
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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 $effectiveGenomeSize.effectiveGenomeSize_opt
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24 #end if
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25
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26 #if str($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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30 ]]>
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31 </command>
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32 <inputs>
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33 <param argument="--GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" help="" />
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34 <param argument="--bamInput" format="bam" type="data"
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35 label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted." />
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36 <expand macro="reference_genome_source" />
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37 <expand macro="effectiveGenomeSize" />
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38 <expand macro="region_limit_operation" />
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39 </inputs>
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40 <outputs>
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41 <data format="bam" from_work_dir="corrected.bam" name="outFileName" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
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46 <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
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47 <param name="ref_source" value="history" />
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48 <param name="input1" value="sequence.2bit" />
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49 <param name="effectiveGenomeSize_opt" value="specific" />
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50 <param name="effectiveGenomeSize" value="23011544" />
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51 <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" />
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52 </test>
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53 </tests>
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54 <help>
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55 <![CDATA[
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56 **What it does**
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57
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58 This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed in
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59 Benjamini and Speed (2012) Nucleic Acids Res.
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60 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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61
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62 You can find more details on the correctGCBias doc page: https://deeptools.readthedocs.org/en/master/content/tools/correctGCBias.html
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63
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64
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65 **Output files**:
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66
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67 - GC-normalized BAM file
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68
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69 -----
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70
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71 @REFERENCES@
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72 ]]>
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73 </help>
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74 <expand macro="citations" />
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75 </tool>