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comparison bedtools_genomecov/genomeCoverageBed.xml @ 3:a48ca51cb2de draft

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author jackcurragh
date Fri, 27 May 2022 10:04:15 +0000
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2:48f8c1265bd9 3:a48ca51cb2de
1 <tool id="bedtools_genomecoveragebed" name="BedTools Genome Coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>Compute Read 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" selected='true'>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>