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comparison bamCoverage.xml @ 18:5ea8782d650c draft

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author bgruening
date Mon, 03 Feb 2014 13:44:35 -0500
parents ef65d6b68ccc
children 69ff16ba27bd
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17:ef65d6b68ccc 18:5ea8782d650c
1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.2"> 1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.3">
2 <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description> 2 <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</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@">bamCoverage</token>
6 <import>deepTools_macros.xml</import> 7 <import>deepTools_macros.xml</import>
7 </macros> 8 </macros>
8 <command> 9 <command>
9 bamCoverage 10 bamCoverage
10 11
19 --binSize $binSize 20 --binSize $binSize
20 21
21 #if $scaling.type=='rpkm': 22 #if $scaling.type=='rpkm':
22 --normalizeUsingRPKM 23 --normalizeUsingRPKM
23 #elif $scaling.type=='1x': 24 #elif $scaling.type=='1x':
24 --normalizeTo1x $scaling.normalizeTo1x 25 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
26 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
27 #else:
28 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
29 #end if
25 #elif $scaling.type=='own': 30 #elif $scaling.type=='own':
26 --scaleFactor $scaling.scaleFactor 31 --scaleFactor $scaling.scaleFactor
32 #end if
33
34 #if str(region).strip() != '':
35 --region 'region'
27 #end if 36 #end if
28 37
29 #if $advancedOpt.showAdvancedOpt == "yes": 38 #if $advancedOpt.showAdvancedOpt == "yes":
30 #if $advancedOpt.smoothLength: 39 #if $advancedOpt.smoothLength:
31 --smoothLength '$advancedOpt.smoothLength' 40 --smoothLength '$advancedOpt.smoothLength'
32 #end if 41 #end if
33 42
34 #if str($advancedOpt.region.value) != '':
35 --region '$advancedOpt.region'
36 #end if
37 $advancedOpt.doNotExtendPairedEnds 43 $advancedOpt.doNotExtendPairedEnds
38 $advancedOpt.ignoreDuplicates 44 $advancedOpt.ignoreDuplicates
39 45
40 #if $advancedOpt.minMappingQuality: 46 #if $advancedOpt.minMappingQuality:
41 --minMappingQuality '$advancedOpt.minMappingQuality' 47 --minMappingQuality '$advancedOpt.minMappingQuality'
68 <option value="no">Do not normalize or scale</option> 74 <option value="no">Do not normalize or scale</option>
69 </param> 75 </param>
70 <when value="rpkm"/> 76 <when value="rpkm"/>
71 <when value="no"/> 77 <when value="no"/>
72 <when value="1x"> 78 <when value="1x">
73 <param name="normalizeTo1x" type="integer" value="2150570000" 79 <expand macro="effectiveGenomeSize" />
74 label="Genome size"
75 help ="Enter the genome size to normalize the reads counts. Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
76 </when> 80 </when>
77 <when value="own"> 81 <when value="own">
78 <param name="scaleFactor" type="float" value="1" size="3" 82 <param name="scaleFactor" type="float" value="1" size="3"
79 label="Scale factor to multiply all values" /> 83 label="Scale factor to multiply all values" />
80 </when> 84 </when>
83 <param name="outFileFormat" type="select" label="Coverage file format"> 87 <param name="outFileFormat" type="select" label="Coverage file format">
84 <option value="bigwig" selected="true">bigwig</option> 88 <option value="bigwig" selected="true">bigwig</option>
85 <option value="bedgraph">bedgraph</option> 89 <option value="bedgraph">bedgraph</option>
86 </param> 90 </param>
87 91
92 <expand macro="region_limit_operation" />
93
88 <conditional name="advancedOpt"> 94 <conditional name="advancedOpt">
89 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 95 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
90 <option value="no" selected="true">no</option> 96 <option value="no" selected="true">no</option>
91 <option value="yes">yes</option> 97 <option value="yes">yes</option>
92 </param> 98 </param>
93 <when value="no" /> 99 <when value="no" />
94 <when value="yes"> 100 <when value="yes">
95 <param name="smoothLength" type="integer" value="1" optional="true" min="1" 101 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
96 label="Smooth values using the following length (in bp)" 102 label="Smooth values using the following length (in bp)"
97 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> 103 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
98
99 <param name="region" type="text" value=""
100 label="Region of the genome to limit the operation to"
101 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;" />
102 104
103 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" 105 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
104 label="Do not extend paired ends" 106 label="Do not extend paired ends"
105 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> 107 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
106 108
138 140
139 141
140 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png 142 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
141 143
142 144
145 You can find more details in the `bamCoverage wiki`_.
146
147 .. _bamCoverage wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage
148
149
143 **Output files**: 150 **Output files**:
144 151
145 - coverage file either in bigWig or bedGraph format 152 - coverage file either in bigWig or bedGraph format
146 153
147 ----- 154 -----
148 155
149 .. class:: infomark
150
151 @REFERENCES@ 156 @REFERENCES@
152 157
153 </help> 158 </help>
154 </tool> 159 </tool>