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