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comparison bigwigCompare.xml @ 18:5ea8782d650c draft

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author bgruening
date Mon, 03 Feb 2014 13:44:35 -0500
parents 135f3bae5c56
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17:ef65d6b68ccc 18:5ea8782d650c
1 <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0.2"> 1 <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0.3">
2 <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description> 2 <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</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@">bigwigCompare</token>
6 <import>deepTools_macros.xml</import> 7 <import>deepTools_macros.xml</import>
7 </macros> 8 </macros>
8 <command> 9 <command>
9 bigwigCompare 10 bigwigCompare
10 11
16 --outFileName '$outFileName' 17 --outFileName '$outFileName'
17 --outFileFormat '$outFileFormat' 18 --outFileFormat '$outFileFormat'
18 19
19 --ratio $comparison_type 20 --ratio $comparison_type
20 21
22 #if str(region).strip() != '':
23 --region 'region'
24 #end if
25
21 #if $advancedOpt.showAdvancedOpt == "yes": 26 #if $advancedOpt.showAdvancedOpt == "yes":
22 #if str($advancedOpt.region.value) != '':
23 --region '$advancedOpt.region'
24 #end if
25 27
26 --missingDataAsZero $advancedOpt.missingDataAsZero 28 --missingDataAsZero $advancedOpt.missingDataAsZero
27 --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2' 29 --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
28 --pseudocount '$advancedOpt.pseudocount' 30 --pseudocount '$advancedOpt.pseudocount'
29 --binSize $advancedOpt.binSize 31 --binSize $advancedOpt.binSize
47 <param name="outFileFormat" type="select" label="Coverage file format"> 49 <param name="outFileFormat" type="select" label="Coverage file format">
48 <option value="bigwig" selected="true">bigwig</option> 50 <option value="bigwig" selected="true">bigwig</option>
49 <option value="bedgraph">bedgraph</option> 51 <option value="bedgraph">bedgraph</option>
50 </param> 52 </param>
51 53
54 <expand macro="region_limit_operation" />
55
52 <conditional name="advancedOpt"> 56 <conditional name="advancedOpt">
53 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 57 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
54 <option value="no" selected="true">no</option> 58 <option value="no" selected="true">no</option>
55 <option value="yes">yes</option> 59 <option value="yes">yes</option>
56 </param> 60 </param>
57 <when value="no" /> 61 <when value="no" />
58 <when value="yes"> 62 <when value="yes">
59 <param name="binSize" type="integer" value="50" min="1" 63 <param name="binSize" type="integer" value="50" min="1"
60 label="Bin size in bp" 64 label="Bin size in bp"
61 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file "/> 65 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file "/>
62
63 <param name="region" type="text" value=""
64 label="Region of the genome to limit the operation to"
65 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;" />
66 66
67 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" 67 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
68 label ="Treat missing data as zero" 68 label ="Treat missing data as zero"
69 help ="This parameter determines if missing data should be replaced with a zero. If set to &quot;no&quot;, missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage." /> 69 help ="This parameter determines if missing data should be replaced with a zero. If set to &quot;no&quot;, missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage." />
70 70
91 compare the bigwig files the genome is partitioned into bins of equal size, 91 compare the bigwig files the genome is partitioned into bins of equal size,
92 then the number of reads found in each BAM file are counted for such bins and 92 then the number of reads found in each BAM file are counted for such bins and
93 finally a summarizing value is reported. This value can be the ratio of the 93 finally a summarizing value is reported. This value can be the ratio of the
94 number of reads per bin, the log2 of the ratio, the sum or the difference. 94 number of reads per bin, the log2 of the ratio, the sum or the difference.
95 95
96
96 ----- 97 -----
97
98 .. class:: infomark
99 98
100 @REFERENCES@ 99 @REFERENCES@
101 100
102 </help> 101 </help>
103 </tool> 102 </tool>