Mercurial > repos > bgruening > deeptools

comparison bamCoverage.xml @ 26:2ad3b027dfcd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Thu, 06 Feb 2014 06:40:05 -0500
parents
children bf1b1dcdd67b
comparison
equal deleted inserted replaced
25:d2898b81b912 26:2ad3b027dfcd
1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.4">
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" />
4 <expand macro="stdio" />
5 <macros>
6 <token name="@BINARY@">bamCoverage</token>
7 <import>deepTools_macros.xml</import>
8 </macros>
9 <command>
10 bamCoverage
11
12 @THREADS@
13
14 --bam '$bamInput'
15 --bamIndex ${bamInput.metadata.bam_index}
16 --outFileName '$outFileName'
17 --outFileFormat '$outFileFormat'
18
19 --fragmentLength $fragmentLength
20 --binSize $binSize
21
22 #if $scaling.type=='rpkm':
23 --normalizeUsingRPKM
24 #elif $scaling.type=='1x':
25 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
26 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
27 #else:
28 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
29 #end if
30 #elif $scaling.type=='own':
31 --scaleFactor $scaling.scaleFactor
32 #end if
33
34 #if str($region).strip() != '':
35 --region '$region'
36 #end if
37
38 #if $advancedOpt.showAdvancedOpt == "yes":
39 #if $advancedOpt.smoothLength:
40 --smoothLength '$advancedOpt.smoothLength'
41 #end if
42
43 $advancedOpt.doNotExtendPairedEnds
44 $advancedOpt.ignoreDuplicates
45
46 #if $advancedOpt.minMappingQuality:
47 --minMappingQuality '$advancedOpt.minMappingQuality'
48 #end if
49
50 ##if str($advancedOpt.ignoreForNormalization).strip() != '':
51 ## --ignoreForNormalization $advancedOpt.ignoreForNormalization
52 ##end if
53
54 #end if
55 </command>
56
57 <inputs>
58 <param name="bamInput" format="bam" type="data" label="BAM file"
59 help="The BAM file must be sorted."/>
60
61 <param name="fragmentLength" type="integer" value="300" min="1"
62 label="Length of the average fragment size"
63 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."/>
64
65 <param name="binSize" type="integer" value="50" min="1"
66 label="Bin size in bp"
67 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. "/>
68
69 <conditional name="scaling">
70 <param name="type" type="select" label="Scaling/Normalization method" >
71 <option value="1x">Normalize coverage to 1x</option>
72 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
73 <option value="own">Set your own scaling factor</option>
74 <option value="no">Do not normalize or scale</option>
75 </param>
76 <when value="rpkm"/>
77 <when value="no"/>
78 <when value="1x">
79 <expand macro="effectiveGenomeSize" />
80 </when>
81 <when value="own">
82 <param name="scaleFactor" type="float" value="1" size="3"
83 label="Scale factor to multiply all values" />
84 </when>
85 </conditional>
86
87 <param name="outFileFormat" type="select" label="Coverage file format">
88 <option value="bigwig" selected="true">bigwig</option>
89 <option value="bedgraph">bedgraph</option>
90 </param>
91
92 <expand macro="region_limit_operation" />
93
94 <conditional name="advancedOpt">
95 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
96 <option value="no" selected="true">no</option>
97 <option value="yes">yes</option>
98 </param>
99 <when value="no" />
100 <when value="yes">
101 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
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."/>
104
105 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
106 label="Do not extend paired ends"
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."/>
108
109 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
110 label="Ignore duplicates"
111 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." />
112
113 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
114 label="Minimum mapping quality"
115 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."/>
116
117 <!-- <param name="ignoreForNormalization" type="text" value="" size="50"
118 label="regions that should be excluded for calculating the scaling factor"
119 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" />
120 -->
121 </when>
122 </conditional>
123 </inputs>
124 <outputs>
125 <data format="bigwig" name="outFileName">
126 <change_format>
127 <when input="outFileFormat" value="bigwig" format="bigwig" />
128 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
129 </change_format>
130 </data>
131 </outputs>
132 <help>
133
134 **What it does**
135
136 Given a BAM file, this tool generates a bigWig or bedGraph file with genome-wide coverage of fragment or read coverages.
137 The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not)
138 that overlap each bin (a region of fixed length, i.e. 25 bp) in the genome. Bins with zero counts are skipped, i.e. not added to the output file.
139 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).
140
141
142 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
143
144
145 You can find more details on the bamCoverage wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage
146
147
148 **Output files**:
149
150 - coverage file either in bigWig or bedGraph format
151
152 -----
153
154 @REFERENCES@
155
156 </help>
157 </tool>