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comparison bamCoverage.xml @ 52:411c871f4cfd

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Uploaded
author bgruening
date Sat, 03 Aug 2013 09:48:44 -0400
parents 6a2a7374450b
children
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51:6a2a7374450b 52:411c871f4cfd
1 <tool id="bamCoverage" name="bamCoverage" version="1.0"> 1 <tool id="bamCoverage" name="bamCoverage" version="1.0">
2 <description>Given a BAM file, generates a coverage bigwig file. Multiple options available to count reads and normalize coverage.</description> 2 <description>Given a BAM file, generates a coverage bigwig file. Multiple options available to count reads and normalize coverage.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement> 4 <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
5 <requirement type="package" version="0.1">ucsc_tools</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement> 6 <requirement type="package" version="1.7.1">numpy</requirement>
6 </requirements> 7 </requirements>
7 <command>bamCoverage 8 <command>bamCoverage
8 --bam '$bamInput' 9 --bam '$bamInput'
9 --bamIndex ${bamInput.metadata.bam_index} 10 --bamIndex ${bamInput.metadata.bam_index}
41 --numberOfProcessors 4 42 --numberOfProcessors 4
42 </command> 43 </command>
43 44
44 <inputs> 45 <inputs>
45 <param name="bamInput" format="bam" type="data" label="Input BAM file" 46 <param name="bamInput" format="bam" type="data" label="Input BAM file"
46 help="The BAM file must be sorted and indexed."/> 47 help="The BAM file must be sorted and indexed."/>
47 48
48 <param name="fragmentLength" type="integer" value="300" min="1" 49 <param name="fragmentLength" type="integer" value="300" min="1"
49 label="Length of the average fragment size" 50 label="Length of the average fragment size"
50 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."/> 51 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."/>
51 52
52 <param name="binSize" type="integer" value="50" min="1" 53 <param name="binSize" type="integer" value="50" min="1"
53 label="Bin size in bp" 54 label="Bin size in bp"
54 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. "/> 55 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. "/>
55 56
56 <conditional name="scaling"> 57 <conditional name="scaling">
57 <param name="type" type="select" label="Scaling/Normalization method" > 58 <param name="type" type="select" label="Scaling/Normalization method" >
58 <option value="1x">Normalize coverage to 1x</option> 59 <option value="1x">Normalize coverage to 1x</option>
59 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option> 60 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
60 <option value="own">Set your own scaling factor</option> 61 <option value="own">Set your own scaling factor</option>
61 <option value="no">Do not normalize or scale</option> 62 <option value="no">Do not normalize or scale</option>
62 </param> 63 </param>
63 <when value="rpkm"/> 64 <when value="rpkm"/>
64 <when value="no"/> 65 <when value="no"/>
65 <when value="1x"> 66 <when value="1x">
66 <param name="normalizeTo1x" type="integer" value="2150570000" 67 <param name="normalizeTo1x" type="integer" value="2150570000"
67 label="Genome size" 68 label="Genome size"
68 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."/> 69 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."/>
69 </when> 70 </when>
70 <when value="own"> 71 <when value="own">
71 <param name="scaleFactor" type="float" value="1" size="3" 72 <param name="scaleFactor" type="float" value="1" size="3"
72 label="Scale factor to multiply all values" /> 73 label="Scale factor to multiply all values" />
73 </when> 74 </when>
74 </conditional> 75 </conditional>
75 76
76 <param name="outFileFormat" type="select" label="Coverage file format"> 77 <param name="outFileFormat" type="select" label="Coverage file format">
77 <option value="bigwig" selected="true">bigwig</option> 78 <option value="bigwig" selected="true">bigwig</option>
78 <option value="bedgraph">bedgraph</option> 79 <option value="bedgraph">bedgraph</option>
79 </param> 80 </param>
80 81
81 82
82 <conditional name="advancedOpt"> 83 <conditional name="advancedOpt">
83 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 84 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
86 </param> 87 </param>
87 <when value="no" /> 88 <when value="no" />
88 <when value="yes"> 89 <when value="yes">
89 90
90 <param name="smoothLength" type="integer" value="1" optional="true" min="1" 91 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
91 label="Smooth values using the following length (in bp)" 92 label="Smooth values using the following length (in bp)"
92 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."/> 93 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."/>
93 94
94 <param name="region" type="text" value="" 95 <param name="region" type="text" value=""
95 label="Region of the genome to limit the operation to" 96 label="Region of the genome to limit the operation to"
96 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;" /> 97 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;" />
97 98
98 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" 99 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
99 label="Do not extend paired ends" 100 label="Do not extend paired ends"
100 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."/> 101 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."/>
101 102
102 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" 103 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
103 label="Ignore duplicates" 104 label="Ignore duplicates"
104 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." /> 105 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." />
105 106
106 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" 107 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
107 label="Minimum mapping quality" 108 label="Minimum mapping quality"
108 help= "If set, only reads that have a mapping quality score higher than the given value are considered"/> 109 help= "If set, only reads that have a mapping quality score higher than the given value are considered"/>
109 </when> 110 </when>
110 </conditional> 111 </conditional>
111 112
112 </inputs> 113 </inputs>
113 <outputs> 114 <outputs>
114 <data format="bigwig" name="outFileName"> 115 <data format="bigwig" name="outFileName">
115 <change_format> 116 <change_format>
116 <when input="outFileFormat" value="bigwig" format="bigwig" /> 117 <when input="outFileFormat" value="bigwig" format="bigwig" />
117 <when input="outFileFormat" value="bedgraph" format="bedgraph" /> 118 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
118 </change_format> 119 </change_format>
119 </data> 120 </data>
120 </outputs> 121 </outputs>
121 <help> 122 <help>
122 123
123 **What it does** 124 **What it does**