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comparison computeGCBias.xml @ 18:5ea8782d650c draft

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author bgruening
date Mon, 03 Feb 2014 13:44:35 -0500
parents 16310f8b24d5
children 69ff16ba27bd
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17:ef65d6b68ccc 18:5ea8782d650c
1 <tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.2"> 1 <tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.3">
2 <description>to see whether your samples should be normalized for GC bias</description> 2 <description>to see whether your samples should be normalized for GC bias</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@">computeGCBias</token>
6 <import>deepTools_macros.xml</import> 7 <import>deepTools_macros.xml</import>
7 </macros> 8 </macros>
8 <command> 9 <command>
9 ln -s $bamInput local_bamInput.bam; 10 ln -s $bamInput local_bamInput.bam;
10 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai; 11 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
22 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize 23 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
23 #else: 24 #else:
24 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt 25 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
25 #end if 26 #end if
26 27
28 #if str(region).strip() != '':
29 --region 'region'
30 #end if
31
27 #if $advancedOpt.showAdvancedOpt == "yes": 32 #if $advancedOpt.showAdvancedOpt == "yes":
28 #if str($advancedOpt.region.value) != '':
29 --region '$advancedOpt.region'
30 #end if
31 33
32 --sampleSize '$advancedOpt.sampleSize' 34 --sampleSize '$advancedOpt.sampleSize'
33 --regionSize '$advancedOpt.regionSize' 35 --regionSize '$advancedOpt.regionSize'
34 36
35 #if $advancedOpt.filterOut: 37 #if $advancedOpt.filterOut:
54 <expand macro="effectiveGenomeSize" /> 56 <expand macro="effectiveGenomeSize" />
55 57
56 <param name="fragmentLength" type="integer" value="300" min="1" 58 <param name="fragmentLength" type="integer" value="300" min="1"
57 label="Fragment length used for the sequencing" 59 label="Fragment length used for the sequencing"
58 help ="If paired-end reads are used, the fragment length is computed from the BAM file."/> 60 help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
61
62 <expand macro="region_limit_operation" />
63
59 <conditional name="advancedOpt"> 64 <conditional name="advancedOpt">
60 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 65 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
61 <option value="no" selected="true">no</option> 66 <option value="no" selected="true">no</option>
62 <option value="yes">yes</option> 67 <option value="yes">yes</option>
63 </param> 68 </param>
64 <when value="no" /> 69 <when value="no" />
65 <when value="yes"> 70 <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="sampleSize" type="integer" value="50000000" min="1" 71 <param name="sampleSize" type="integer" value="50000000" min="1"
71 label="Number of sampling points to be considered" /> 72 label="Number of sampling points to be considered" />
72 73
73 <param name="regionSize" type="integer" value="300" min="1" 74 <param name="regionSize" type="integer" value="300" min="1"
74 label="Region size" 75 label="Region size"
129 usually shows a significant bias towards reads with high GC content (>50%) 130 usually shows a significant bias towards reads with high GC content (>50%)
130 131
131 .. image:: $PATH_TO_IMAGES/QC_GCplots_input.png 132 .. image:: $PATH_TO_IMAGES/QC_GCplots_input.png
132 133
133 134
135 You can find more details in the `computeGCBias wiki`_.
136
137 .. _computeGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias
138
139
134 **Output files**: 140 **Output files**:
135 141
136 - Diagnostic plot 142 - Diagnostic plot
137 143
138 - box plot of absolute read numbers per genomic GC bin 144 - box plot of absolute read numbers per genomic GC bin
143 - to be used for GC correction with correctGCbias 149 - to be used for GC correction with correctGCbias
144 150
145 151
146 ----- 152 -----
147 153
148 .. class:: infomark
149
150 @REFERENCES@ 154 @REFERENCES@
151 155
152 </help> 156 </help>
153 </tool> 157 </tool>