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comparison coverageBed.xml @ 0:4cacc5b8001b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
author pimarin
date Thu, 23 Feb 2023 09:50:24 +0000
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-1:000000000000 0:4cacc5b8001b
1 <tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>of features in file B on the features in file A (bedtools coverage)</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tools" />
7 <expand macro="requirements">
8 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
9 </expand>
10 <expand macro="stdio" />
11 <command><![CDATA[
12 bedtools coverage
13 $d
14 $hist
15 $split
16 $strandedness
17 $mean
18 #if str($overlap_a):
19 -f $overlap_a
20 #end if
21 #if str($overlap_b):
22 -F $overlap_b
23 #end if
24 $reciprocal_overlap
25 $a_or_b
26 -a '$inputA'
27 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
28 -b '$reduce_or_iterate.inputB'
29 #else:
30 -b
31 #for $file in $reduce_or_iterate.inputB
32 '$file'
33 #end for
34 #end if
35 @SORTED@
36 #if $inputA.is_of_type('gff'):
37 | sort -k1,1 -k4,2n
38 #else:
39 | sort -k1,1 -k2,2n
40 #end if
41 > '$output'
42 ]]></command>
43 <inputs>
44 <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
45 <conditional name="reduce_or_iterate">
46 <param name="reduce_or_iterate_selector" type="select" label="Combined or separate output files">
47 <option value="iterate" selected="true">One output file per 'input B' file</option>
48 <option value="reduce">Single output containing results for all 'input B' files</option>
49 </param>
50 <when value="iterate">
51 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@"
52 label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
53 </when>
54 <when value="reduce">
55 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true"
56 label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
57 </when>
58 </conditional>
59 <expand macro="split" />
60 <param name="strandedness" argument="-s" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
61 help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/>
62 <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
63 label="Report the depth at each position in each A feature"
64 help="Positions reported are one based. Each position and depth follow the complete B feature" />
65 <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"
66 label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
67 help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" />
68 <param name="mean" argument="-mean" type="boolean" label="Mean depth" truevalue="-mean" falsevalue="" checked="false"
69 help="Report the mean depth of all positions in each A feature."/>
70 <expand macro="overlap" name="overlap_a" />
71 <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />
72 <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
73 label="Require that the fraction overlap be reciprocal for A AND B."
74 help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B" />
75 <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
76 label="Require that the minimum fraction be satisfied for A OR B."
77 help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied" />
78 <!-- -sorted -g -->
79 <expand macro="sorted" />
80 </inputs>
81 <outputs>
82 <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
83 </outputs>
84 <tests>
85 <test>
86 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
87 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
88 <output name="output" file="coverageBed_result1.bed" ftype="bed" />
89 </test>
90 <test>
91 <param name="inputA" value="multiCov1.bed" ftype="bed" />
92 <param name="inputB" value="srma_in3.bam" ftype="bam" />
93 <param name="sorted" value="true"/>
94 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
95 </test>
96 <test>
97 <param name="inputA" value="multiCov1.bed" ftype="bed" />
98 <param name="reduce_or_iterate_selector" value="reduce" />
99 <param name="inputB" value="srma_in3.bam" ftype="bam" />
100 <param name="sorted" value="true"/>
101 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
102 </test>
103 <test>
104 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
105 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
106 <param name="overlap_b" value="1" />
107 <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
108 </test>
109 <test>
110 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
111 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
112 <param name="overlap_a" value="1E-5" />
113 <param name="reciprocal_overlap" value="true" />
114 <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
115 </test>
116 <test>
117 <param name="inputA" value="multiCov1.bed" ftype="bed" />
118 <param name="reduce_or_iterate_selector" value="reduce" />
119 <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" />
120 <param name="sorted" value="true"/>
121 <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" />
122 </test>
123 <test>
124 <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
125 <param name="inputB" value="coverageBed.bam" ftype="bam" />
126 <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
127 </test>
128 <test>
129 <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
130 <param name="inputB" value="coverageBed.bam" ftype="bam" />
131 <param name="mean" value="true"/>
132 <output name="output" file="mean_coverage.bed" ftype="bed" />
133 </test>
134 </tests>
135 <help><![CDATA[
136 **What it does**
137
138 `bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in
139 file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments
140 (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest.
141 One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that
142 overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features.
143 Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.
144
145 .. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
146
147 .. class:: infomark
148
149 The lines in the output will be comprised of each interval in A, followed by:
150
151 1. The number of features in B that overlapped (by at least one base pair) the A interval.
152 2. The number of bases in A that had non-zero coverage from features in B.
153 3. The length of the entry in A.
154 4. The fraction of bases in A that had non-zero coverage from features in B.
155
156 @REFERENCES@
157 ]]></help>
158 <expand macro="citations" />
159 </tool>