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comparison correctGCBias.xml @ 110:fa6ef7619bbd draft default tip

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author bgruening
date Mon, 26 Jan 2015 13:10:16 -0500
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1 <tool id="deeptools_correctGCBias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
2 <description>uses the output from computeGCBias to generate corrected BAM files</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros>
6 <token name="@BINARY@">correctGCBias</token>
7 <import>deepTools_macros.xml</import>
8 </macros>
9 <command>
10 <![CDATA[
11 ln -s $bamInput local_bamInput.bam;
12 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
13
14 correctGCBias
15 @THREADS@
16 --bamfile local_bamInput.bam
17 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
18
19 @reference_genome_source@
20
21 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
22 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
23 #else:
24 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
25 #end if
26
27 #if str($region).strip() != '':
28 --region '$region'
29 #end if
30 --correctedFile $outFileName
31 ]]>
32 </command>
33 <inputs>
34 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
35 <param name="bamInput" format="bam" type="data"
36 label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
37 <expand macro="reference_genome_source" />
38 <expand macro="effectiveGenomeSize" />
39 <expand macro="region_limit_operation" />
40 </inputs>
41 <outputs>
42 <data format="bam" name="outFileName" />
43 </outputs>
44 <tests>
45 <test>
46 <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
47 <param name="bamInput" value="phiX.bam" ftype="bam" />
48 <param name="ref_source" value="history" />
49 <param name="input1" value="phiX.2bit" />
50 <param name="effectiveGenomeSize_opt" value="specific" />
51 <param name="effectiveGenomeSize" value="5386" />
52 <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" compare="sim_size" />
53 </test>
54 </tests>
55 <help>
56 <![CDATA[
57 **What it does**
58
59 This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by
60 Benjamini and Speed (2012) Nucleic Acids Res.
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.
62
63 You can find more details on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
64
65
66 **Output files**:
67
68 - GC-normalized BAM file
69
70 -----
71
72 @REFERENCES@
73 ]]>
74 </help>
75 <expand macro="citations" />
76 </tool>