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comparison genomeCoverageBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
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0:b8348686a0b9 1:82aac94b06c3
1 <tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0">
2 <description>in bedGraph or histogram format</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 <![CDATA[
10 bedtools genomecov
11 #if $input.ext == "bam"
12 -ibam '$input'
13 #else
14 -i '$input'
15 -g $genome
16 #end if
17
18 $split
19 $strand
20
21 #if str($report.report_select) == "bg":
22 #if $zero_regions.value:
23 $zero_regions
24 #else:
25 -bg
26 #end if
27
28 #if str($scale):
29 -scale $scale
30 #end if
31 #else:
32 #if str($report.max):
33 -max $report.max
34 #end if
35 #end if
36 $d
37 $dz
38 $five
39 $three
40
41 > '$output'
42 ]]>
43 </command>
44 <inputs>
45 <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed">
46 <validator type="unspecified_build" />
47 </param>
48 <conditional name="report">
49 <param name="report_select" type="select" label="Output type">
50 <option value="bg" selected="true">BedGraph coverage file</option>
51 <option value="hist">Data suiteable for Histogram</option>
52 </param>
53 <when value="bg">
54 <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue=""
55 label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. (-bga)" />
56 <param name="scale" type="float" value="1.0"
57 label="Scale the coverage by a constant factor"
58 help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)"/>
59 </when>
60 <when value="hist">
61 <param name="max" type="integer" label="Specify max depth" value="0"
62 help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/>
63 </when>
64 </conditional>
65 <expand macro="genome" />
66 <expand macro="split" />
67 <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)">
68 <option value="">both strands combined</option>
69 <option value="-strand +">positive strand only</option>
70 <option value="-strand -">negative strand only</option>
71 </param>
72
73 <param name="d" type="boolean" checked="False" truevalue="-d" falsevalue=""
74 label="Report the depth at each genome position with 1-based coordinates" help="(-d)" />
75 <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue=""
76 label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" />
77 <param name="five" type="boolean" checked="False" truevalue="-d" falsevalue=""
78 label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" />
79 <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue=""
80 label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" />
81 </inputs>
82 <outputs>
83 <data format="bedgraph" name="output">
84 <change_format>
85 <when input="report.report_select" value="hist" format="tabular" />
86 </change_format>
87 </data>
88 </outputs>
89 <tests>
90 <test>
91 <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
92 <param name="genome" value="genomeCoverageBed1.len" />
93 <param name="report_select" value="hist" />
94 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
95 </test>
96 </tests>
97 <help>
98 <![CDATA[
99 **What it does**
100
101 This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format.
102
103 .. image:: $PATH_TO_IMAGES/genomecov-glyph.png
104
105 .. class:: warningmark
106
107 The input BED or BAM file must be sorted by chromosome name (but doesn't necessarily have to be sorted by start position).
108
109 -----
110
111 **Example 1**
112
113 Input (BED format)-
114 Overlapping, un-sorted intervals::
115
116 chr1 140 176
117 chr1 100 130
118 chr1 120 147
119
120
121 Output (BedGraph format)-
122 Sorted, non-overlapping intervals, with coverage value on the 4th column::
123
124 chr1 100 120 1
125 chr1 120 130 2
126 chr1 130 140 1
127 chr1 140 147 2
128 chr1 147 176 1
129
130 -----
131
132 **Example 2 - with ZERO-Regions selected (assuming hg19)**
133
134 Input (BED format)-
135 Overlapping, un-sorted intervals::
136
137 chr1 140 176
138 chr1 100 130
139 chr1 120 147
140
141
142 BedGraph output will contain five columns:
143
144 * 1. Chromosome name (or 'genome' for whole-genome coverage)
145 * 2. Coverage depth
146 * 3. The number of bases on chromosome (or genome) with depth equal to column 2.
147 * 4. The size of chromosome (or entire genome) in base pairs
148 * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.
149
150 **Example Output**:
151
152 chr2L 0 1379895 23011544 0.0599653
153 chr2L 1 837250 23011544 0.0363839
154 chr2L 2 904442 23011544 0.0393038
155 chr2L 3 913723 23011544 0.0397072
156 chr2L 4 952166 23011544 0.0413778
157 chr2L 5 967763 23011544 0.0420555
158 chr2L 6 986331 23011544 0.0428624
159 chr2L 7 998244 23011544 0.0433801
160 chr2L 8 995791 23011544 0.0432735
161 chr2L 9 996398 23011544 0.0432999
162
163
164 @REFERENCES@
165 ]]>
166 </help>
167 <expand macro="citations" />
168 </tool>