annotate bamCoverage.xml @ 6:1ee0b1ecf500 draft

Uploaded
author bgruening
date Mon, 02 Dec 2013 07:49:06 -0500
parents d957e25e18a3
children c53a73b8eef9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
2 <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
3 <expand macro="requirements" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
4 <macros>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
5 <import>deepTools_macros.xml</import>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
6 </macros>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
7 <command>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
8 bamCoverage
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
9
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
10 @THREADS@
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
11
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
12 --bam '$bamInput'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
13 --bamIndex ${bamInput.metadata.bam_index}
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
14 --outFileName '$outFileName'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
15 --outFileFormat '$outFileFormat'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
16
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
17 --fragmentLength $fragmentLength
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
18 --binSize $binSize
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
19
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
20 #if $scaling.type=='rpkm':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
21 --normalizeUsingRPKM
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
22 #elif $scaling.type=='1x':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
23 --normalizeTo1x $scaling.normalizeTo1x
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
24 #elif $scaling.type=='own':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
25 --scaleFactor $scaling.scaleFactor
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
26 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
27
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
28 ##if str($ignoreForNormalization).strip() != '':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
29 ## --ignoreForNormalization $ignoreForNormalization
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
30 ##end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
31
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
32 #if $advancedOpt.showAdvancedOpt == "yes":
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
33 #if $advancedOpt.smoothLength:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
34 --smoothLength '$advancedOpt.smoothLength'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
35 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
36
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
37 #if str($advancedOpt.region.value) != '':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
38 --region '$advancedOpt.region'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
39 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
40 $advancedOpt.doNotExtendPairedEnds
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
41 $advancedOpt.ignoreDuplicates
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
42
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
43 #if $advancedOpt.minMappingQuality:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
44 --minMappingQuality '$advancedOpt.minMappingQuality'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
45 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
46
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
47 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
48 </command>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
49
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
50 <inputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
51 <param name="bamInput" format="bam" type="data" label="Input BAM file"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
52 help="The BAM file must be sorted."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
53
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
54 <param name="fragmentLength" type="integer" value="300" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
55 label="Length of the average fragment size"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
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."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
57
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
58 <param name="binSize" type="integer" value="50" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
59 label="Bin size in bp"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
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. "/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
61
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
62 <conditional name="scaling">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
63 <param name="type" type="select" label="Scaling/Normalization method" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
64 <option value="1x">Normalize coverage to 1x</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
65 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
66 <option value="own">Set your own scaling factor</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
67 <option value="no">Do not normalize or scale</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
68 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
69 <when value="rpkm"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
70 <when value="no"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
71 <when value="1x">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
72 <param name="normalizeTo1x" type="integer" value="2150570000"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
73 label="Genome size"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
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."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
75 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
76 <when value="own">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
77 <param name="scaleFactor" type="float" value="1" size="3"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
78 label="Scale factor to multiply all values" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
79 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
80 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
81
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
82 <!--
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
83 Not yet supported.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
84 <param name="ignoreForNormalization" type="text" value="" size="50"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
85 label="regions that should be excluded for calculating the scaling factor"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
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" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
87 -->
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
88
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
89 <param name="outFileFormat" type="select" label="Coverage file format">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
90 <option value="bigwig" selected="true">bigwig</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
91 <option value="bedgraph">bedgraph</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
92 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
93
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
94 <conditional name="advancedOpt">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
95 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
96 <option value="no" selected="true">no</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
97 <option value="yes">yes</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
98 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
99 <when value="no" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
100 <when value="yes">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
101 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
102 label="Smooth values using the following length (in bp)"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
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."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
104
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
105 <param name="region" type="text" value=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
106 label="Region of the genome to limit the operation to"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
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;" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
108
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
109 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
110 label="Do not extend paired ends"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
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."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
112
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
113 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
114 label="Ignore duplicates"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
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." />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
116
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
117 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
118 label="Minimum mapping quality"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
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."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
120 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
121 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
122 </inputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
123 <outputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
124 <data format="bigwig" name="outFileName">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
125 <change_format>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
126 <when input="outFileFormat" value="bigwig" format="bigwig" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
127 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
128 </change_format>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
129 </data>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
130 </outputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
131 <help>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
132
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
133 **What it does**
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
134
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
135 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or read coverages.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
136 The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not)
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
137 that overlap each bin in the genome. Bins with zero counts are skipped, i.e. not added to the output file.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
138 The resulting read counts can be normalized using either a given scaling factor, the RPKM formula or to get a 1x depth of coverage (RPGC).
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
139
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
140
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
141 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
142
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
143
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
144 **Output files**:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
145
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
146 - coverage file either in bigWig or bedGraph format
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
147
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
148 -----
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
149
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
150 .. class:: infomark
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
151
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
152 @REFERENCES@
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
153
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
154 </help>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
155 </tool>