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comparison bamCoverage.xml @ 14:b0d64a9930d6 draft

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author bgruening
date Thu, 14 Nov 2013 05:43:15 -0500
parents a68a771625d2
children 8436c195dd6c
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13:06311d89da81 14:b0d64a9930d6
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
7 <command> 7 <command>
8 bamCoverage 8 bamCoverage
9 9
10 @THREADS@ 10 @THREADS@
11 11
12 --bam '$bamInput' 12 --bam '$bamInput'
13 --bamIndex ${bamInput.metadata.bam_index} 13 --bamIndex ${bamInput.metadata.bam_index}
14 --outFileName '$outFileName' 14 --outFileName '$outFileName'
15 --outFileFormat '$outFileFormat' 15 --outFileFormat '$outFileFormat'
16 16
17 --fragmentLength $fragmentLength 17 --fragmentLength $fragmentLength
18 --binSize $binSize 18 --binSize $binSize
19 19
20 #if $scaling.type=='rpkm': 20 #if $scaling.type=='rpkm':
21 --normalizeUsingRPKM 21 --normalizeUsingRPKM
22 #elif $scaling.type=='1x': 22 #elif $scaling.type=='1x':
23 --normalizeTo1x $scaling.normalizeTo1x 23 --normalizeTo1x $scaling.normalizeTo1x
24 #elif $scaling.type=='own': 24 #elif $scaling.type=='own':
25 --scaleFactor $scaling.scaleFactor 25 --scaleFactor $scaling.scaleFactor
26 #end if 26 #end if
27 27
28 ##if str($ignoreForNormalization).strip() != '': 28 ##if str($ignoreForNormalization).strip() != '':
29 ## --ignoreForNormalization $ignoreForNormalization 29 ## --ignoreForNormalization $ignoreForNormalization
30 ##end if 30 ##end if
31 31
32 #if $advancedOpt.showAdvancedOpt == "yes": 32 #if $advancedOpt.showAdvancedOpt == "yes":
33 #if $advancedOpt.smoothLength: 33 #if $advancedOpt.smoothLength:
34 --smoothLength '$advancedOpt.smoothLength' 34 --smoothLength '$advancedOpt.smoothLength'
35 #end if 35 #end if
36 36
37 #if str($advancedOpt.region.value) != '': 37 #if str($advancedOpt.region.value) != '':
38 --region '$advancedOpt.region' 38 --region '$advancedOpt.region'
39 #end if 39 #end if
40 $advancedOpt.doNotExtendPairedEnds 40 $advancedOpt.doNotExtendPairedEnds
41 $advancedOpt.ignoreDuplicates 41 $advancedOpt.ignoreDuplicates
42 42
43 #if $advancedOpt.minMappingQuality: 43 #if $advancedOpt.minMappingQuality:
44 --minMappingQuality '$advancedOpt.minMappingQuality' 44 --minMappingQuality '$advancedOpt.minMappingQuality'
45 #end if 45 #end if
46 46
47 #end if 47 #end if
48 </command> 48 </command>
49 49
50 <inputs> 50 <inputs>
51 <param name="bamInput" format="bam" type="data" label="Input BAM file" 51 <param name="bamInput" format="bam" type="data" label="Input BAM file"
52 help="The BAM file must be sorted."/> 52 help="The BAM file must be sorted."/>
53 53
54 <param name="fragmentLength" type="integer" value="300" min="1" 54 <param name="fragmentLength" type="integer" value="300" min="1"
55 label="Length of the average fragment size" 55 label="Length of the average fragment size"
56 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> 56 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>
57 57
58 <param name="binSize" type="integer" value="50" min="1" 58 <param name="binSize" type="integer" value="50" min="1"
59 label="Bin size in bp" 59 label="Bin size in bp"
60 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/> 60 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
61 61
62 <conditional name="scaling"> 62 <conditional name="scaling">
63 <param name="type" type="select" label="Scaling/Normalization method" > 63 <param name="type" type="select" label="Scaling/Normalization method" >
64 <option value="1x">Normalize coverage to 1x</option> 64 <option value="1x">Normalize coverage to 1x</option>
65 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option> 65 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
66 <option value="own">Set your own scaling factor</option> 66 <option value="own">Set your own scaling factor</option>
67 <option value="no">Do not normalize or scale</option> 67 <option value="no">Do not normalize or scale</option>
68 </param> 68 </param>
69 <when value="rpkm"/> 69 <when value="rpkm"/>
70 <when value="no"/> 70 <when value="no"/>
71 <when value="1x"> 71 <when value="1x">
72 <param name="normalizeTo1x" type="integer" value="2150570000" 72 <param name="normalizeTo1x" type="integer" value="2150570000"
73 label="Genome size" 73 label="Genome size"
74 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."/> 74 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."/>
75 </when> 75 </when>
76 <when value="own"> 76 <when value="own">
77 <param name="scaleFactor" type="float" value="1" size="3" 77 <param name="scaleFactor" type="float" value="1" size="3"
78 label="Scale factor to multiply all values" /> 78 label="Scale factor to multiply all values" />
79 </when> 79 </when>
80 </conditional> 80 </conditional>
81 81
82 <!-- 82 <!--
83 Not yet supported. 83 Not yet supported.
84 <param name="ignoreForNormalization" type="text" value="" size="50" 84 <param name="ignoreForNormalization" type="text" value="" size="50"
85 label="regions that should be excluded for calculating the scaling factor" 85 label="regions that should be excluded for calculating the scaling factor"
86 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" /> 86 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
87 --> 87 -->
88 88
89 <param name="outFileFormat" type="select" label="Coverage file format"> 89 <param name="outFileFormat" type="select" label="Coverage file format">
90 <option value="bigwig" selected="true">bigwig</option> 90 <option value="bigwig" selected="true">bigwig</option>
91 <option value="bedgraph">bedgraph</option> 91 <option value="bedgraph">bedgraph</option>
92 </param> 92 </param>
93 93
94 <conditional name="advancedOpt"> 94 <conditional name="advancedOpt">
95 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 95 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
96 <option value="no" selected="true">no</option> 96 <option value="no" selected="true">no</option>
97 <option value="yes">yes</option> 97 <option value="yes">yes</option>
98 </param> 98 </param>
99 <when value="no" /> 99 <when value="no" />
100 <when value="yes"> 100 <when value="yes">
101 <param name="smoothLength" type="integer" value="1" optional="true" min="1" 101 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
102 label="Smooth values using the following length (in bp)" 102 label="Smooth values using the following length (in bp)"
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."/> 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."/>
104 104
105 <param name="region" type="text" value="" 105 <param name="region" type="text" value=""
106 label="Region of the genome to limit the operation to" 106 label="Region of the genome to limit the operation to"
107 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;" /> 107 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;" />
108 108
109 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" 109 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
110 label="Do not extend paired ends" 110 label="Do not extend paired ends"
111 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."/> 111 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."/>
112 112
113 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" 113 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
114 label="Ignore duplicates" 114 label="Ignore duplicates"
115 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 115 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
116 116
117 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" 117 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
118 label="Minimum mapping quality" 118 label="Minimum mapping quality"
119 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> 119 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
120 </when> 120 </when>
121 </conditional> 121 </conditional>
122 </inputs> 122 </inputs>
123 <outputs> 123 <outputs>
124 <data format="bigwig" name="outFileName"> 124 <data format="bigwig" name="outFileName">
125 <change_format> 125 <change_format>
126 <when input="outFileFormat" value="bigwig" format="bigwig" /> 126 <when input="outFileFormat" value="bigwig" format="bigwig" />
127 <when input="outFileFormat" value="bedgraph" format="bedgraph" /> 127 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
128 </change_format> 128 </change_format>
129 </data> 129 </data>
130 </outputs> 130 </outputs>
131 <help> 131 <help>
132 132
133 **What it does** 133 **What it does**
134 134
135 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or read coverages. 135 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or read coverages.
136 The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not) 136 The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not)