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comparison correctGCBias.xml @ 18:5ea8782d650c draft

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author bgruening
date Mon, 03 Feb 2014 13:44:35 -0500
parents b4c5dd45778a
children 69ff16ba27bd
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17:ef65d6b68ccc 18:5ea8782d650c
1 <tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.2"> 1 <tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.3">
2 <description>uses the output from computeGCBias to generate corrected BAM files</description> 2 <description>uses the output from computeGCBias to generate corrected BAM files</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <expand macro="stdio" /> 4 <expand macro="stdio" />
5 <macros> 5 <macros>
6 <token name="@BINARY@">correctGCBias</token>
6 <import>deepTools_macros.xml</import> 7 <import>deepTools_macros.xml</import>
7 </macros> 8 </macros>
8 <command> 9 <command>
9 #import tempfile 10 #import tempfile
10 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) 11 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
30 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize 31 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
31 #else: 32 #else:
32 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt 33 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
33 #end if 34 #end if
34 35
36 #if str(region).strip() != '':
37 --region 'region'
38 #end if
39
35 #if $advancedOpt.showAdvancedOpt == "yes": 40 #if $advancedOpt.showAdvancedOpt == "yes":
36 #if str($advancedOpt.region.value) != '':
37 --region '$advancedOpt.region'
38 #end if
39 --binSize '$advancedOpt.binSize' 41 --binSize '$advancedOpt.binSize'
40 #end if 42 #end if
41 43
42 #set newoutFileName="corrected."+str($outFileFormat) 44 ###set newoutFileName="corrected."+str($outFileFormat)
43 --correctedFile $newoutFileName; 45 ##--correctedFile $newoutFileName;
46 --correctedFile "corrected.bam";
44 47
45 mv $newoutFileName $outFileName 48 mv $newoutFileName $outFileName
46 </command> 49 </command>
47 <inputs> 50 <inputs>
48 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" /> 51 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
49 <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/> 52 <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
50 <expand macro="reference_genome_source" /> 53 <expand macro="reference_genome_source" />
51 <expand macro="effectiveGenomeSize" /> 54 <expand macro="effectiveGenomeSize" />
52 55
56 <!--
53 <param name="outFileFormat" type="select" label="File format of the output"> 57 <param name="outFileFormat" type="select" label="File format of the output">
54 <option value="bam">bam</option> 58 <option value="bam">bam</option>
55 <option value="bw">bigwig</option> 59 <option value="bw">bigwig</option>
56 <option value="bg">bedgraph</option> 60 <option value="bg">bedgraph</option>
57 </param> 61 </param>
62 -->
63 <expand macro="region_limit_operation" />
58 64
59 <conditional name="advancedOpt"> 65 <conditional name="advancedOpt">
60 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 66 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
61 <option value="no" selected="true">no</option> 67 <option value="no" selected="true">no</option>
62 <option value="yes">yes</option> 68 <option value="yes">yes</option>
63 </param> 69 </param>
64 <when value="no" /> 70 <when value="no" />
65 <when value="yes"> 71 <when value="yes">
66 <param name="region" type="text" value=""
67 label="Region of the genome to limit the operation to"
68 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
69
70 <param name="binSize" type="integer" value="50" min="1" 72 <param name="binSize" type="integer" value="50" min="1"
71 label="Bin size in bp" 73 label="Bin size in bp"
72 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/> 74 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
73 </when> 75 </when>
74 </conditional> 76 </conditional>
75 </inputs> 77 </inputs>
76 <outputs> 78 <outputs>
77 <data format="bam" name="outFileName"> 79 <data format="bam" name="outFileName">
78 <change_format> 80 <!--<change_format>
79 <when input="outFileFormat" value="bw" format="bigwig" /> 81 <when input="outFileFormat" value="bw" format="bigwig" />
80 <when input="outFileFormat" value="bam" format="bam" /> 82 <when input="outFileFormat" value="bam" format="bam" />
81 <when input="outFileFormat" value="bg" format="bedgraph" /> 83 <when input="outFileFormat" value="bg" format="bedgraph" />
82 </change_format> 84 </change_format>-->
83 </data> 85 </data>
84 </outputs> 86 </outputs>
85 <help> 87 <help>
86 88
87 **What it does** 89 **What it does**
88 90
89 This tool requires the output from computeGCBias to correct the given BAM files according to the method proposed by Benjamini and Speed (2012). Nucleic Acids Res. 91 This tool requires the output from computeGCBias to correct the given BAM files according to the method proposed by Benjamini and Speed (2012). Nucleic Acids Res.
90 The resulting BAM files can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on. 92 The resulting BAM files can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.
91 93
94
95 You can find more details in the `correctGCBias wiki`_.
96
97 .. _correctGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
98
99
92 **Output files**: 100 **Output files**:
93 101
94 - GC-normalized BAM file 102 - GC-normalized BAM file
95 103
96 ----- 104 -----
97 105
98 .. class:: infomark
99
100 @REFERENCES@ 106 @REFERENCES@
101 107
102 </help> 108 </help>
103 </tool> 109 </tool>