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comparison bamCorrelate.xml @ 28:f7712a057440 draft

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new bugfix release
author bgruening
date Wed, 02 Apr 2014 09:15:44 -0400
parents bf1b1dcdd67b
children 3a2aab18a217
comparison
equal deleted inserted replaced
27:bf1b1dcdd67b 28:f7712a057440
1 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.5"> 1 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="@WRAPPER_VERSION@.0">
2 <description>correlates pairs of BAM files</description> 2 <description>correlates pairs of BAM files</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@">bamCorrelate</token> 6 <token name="@BINARY@">bamCorrelate</token>
33 --plotFileFormat 'png' 33 --plotFileFormat 'png'
34 #end if 34 #end if
35 35
36 #if $mode.modeOpt == "bins": 36 #if $mode.modeOpt == "bins":
37 --binSize '$mode.binSize' 37 --binSize '$mode.binSize'
38 --numberOfSamples '$mode.numberOfSamples' 38 --distanceBetweenBins '$mode.distanceBetweenBins'
39 $mode.doNotRemoveOutliers
40
39 #else: 41 #else:
40 --BED $mode.region_file 42 --BED $mode.region_file
41 #end if 43 #end if
42 44
43 #### options available in both modes 45 #### options available in both modes
72 <param name="fragmentLength" type="integer" value="300" min="1" 74 <param name="fragmentLength" type="integer" value="300" min="1"
73 label="Length of the average fragment size" 75 label="Length of the average fragment size"
74 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. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> 76 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. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>
75 77
76 <param name="corMethod" type="select" label="Correlation method"> 78 <param name="corMethod" type="select" label="Correlation method">
79 <option value="spearman" selected="True">Spearman</option>
77 <option value="pearson">Pearson</option> 80 <option value="pearson">Pearson</option>
78 <option value="spearman">Spearman</option>
79 </param> 81 </param>
80 82
81 <conditional name="mode"> 83 <conditional name="mode">
82 <param name="modeOpt" type="select" label="Choose computation mode" 84 <param name="modeOpt" type="select" label="Choose computation mode"
83 help="In the bins mode, the correlation is computed based on equal length bins. In the BED file mode, as list of genomic regions in BED format has to be given. For each region in the BED file the number of overlapping reads is counted in each of the BAM files. Then the correlation is computed."> 85 help="In the bins mode, the correlation is computed based on equal length bins. In the BED file mode, as list of genomic regions in BED format has to be given. For each region in the BED file the number of overlapping reads is counted in each of the BAM files. Then the correlation is computed.">
87 <when value="bins"> 89 <when value="bins">
88 <param name="binSize" type="integer" value="10000" min="1" 90 <param name="binSize" type="integer" value="10000" min="1"
89 label="Bin size in bp" 91 label="Bin size in bp"
90 help="Length in base pairs for a window used to sample the genome."/> 92 help="Length in base pairs for a window used to sample the genome."/>
91 93
92 <param name="numberOfSamples" type="integer" value="100000" min="1" 94 <param name="distanceBetweenBins" type="integer" value="0" min="0"
93 label="Number of samples" 95 label="Distance between bins"
94 help="Number of samples taken from the genome to compute the scaling factors"/> 96 help="By default, bamCorrelate considers consecutive bins of
97 the specified 'Bin size'. However, to reduce the
98 computation time, a larger distance between bins can
99 by given. Larger distances result in less bins being
100 considered"/>
101
102 <param name="doNotRemoveOutliers" type="boolean"
103 truevalue="--doNotRemoveOutliers" falsevalue="" label="Do not filter outliers"
104 help="By default, bins with very large counts are removed.
105 By setting this option, outliers will not be
106 removed. Bins with unusually large counts normally
107 correspond to regions in the genome that accumulate
108 lot of reads like satellite regions. If outliers are not
109 removed the pearson correlation will wrongly report a
110 very high correlation; that's why, by default,
111 bamCorrelate tries to remove outliers using
112 the median absolute deviation (MAD) method applying a
113 threshold of 200 to only consider extremely large
114 deviations from the median."/>
115
95 <expand macro="bamCorrelate_mode_actions" /> 116 <expand macro="bamCorrelate_mode_actions" />
96 </when> 117 </when>
97 <when value="BED-file"> 118 <when value="BED-file">
98 <param name="region_file" type="data" format="bed" label="Region file in BED format" help="Correlation is computed for the number of reads that overlap such regions."/> 119 <param name="region_file" type="data" format="bed" label="Region file in BED format" help="Correlation is computed for the number of reads that overlap such regions."/>
99 <expand macro="bamCorrelate_mode_actions" /> 120 <expand macro="bamCorrelate_mode_actions" />