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comparison coverageBed.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 7411007544bf
children
comparison
equal deleted inserted replaced
63:7411007544bf 64:f6c88d2e9ae5
1 <tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>of features in file B on the features in file A (bedtools coverage)</description> 2 <description>of features in file B on the features in file A (bedtools coverage)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools" /> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> 8 <requirement type="package" version="1.18">samtools</requirement>
9 </expand> 9 </expand>
10 <expand macro="stdio" /> 10 <expand macro="stdio"/>
11 <command><![CDATA[ 11 <command><![CDATA[
12 bedtools coverage 12 bedtools coverage
13 $d 13 $d
14 $hist 14 $hist
15 $split 15 $split
39 | sort -k1,1 -k2,2n 39 | sort -k1,1 -k2,2n
40 #end if 40 #end if
41 > '$output' 41 > '$output'
42 ]]></command> 42 ]]></command>
43 <inputs> 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" /> 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"> 45 <conditional name="reduce_or_iterate">
46 <param name="reduce_or_iterate_selector" type="select" label="Combined or separate output files"> 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> 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> 48 <option value="reduce">Single output containing results for all 'input B' files</option>
49 </param> 49 </param>
50 <when value="iterate"> 50 <when value="iterate">
51 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" 51 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
52 label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
53 </when> 52 </when>
54 <when value="reduce"> 53 <when value="reduce">
55 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true" 54 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" multiple="true"/>
56 label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
57 </when> 55 </when>
58 </conditional> 56 </conditional>
59 <expand macro="split" /> 57 <expand macro="split"/>
60 <param name="strandedness" argument="-s" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 58 <param name="strandedness" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness" help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/>
61 help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/> 59 <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" label="Report the depth at each position in each A feature" help="Positions reported are one based. Each position and depth follow the complete B feature"/>
62 <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" 60 <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false" label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A" help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth"/>
63 label="Report the depth at each position in each A feature" 61 <param argument="-mean" type="boolean" truevalue="-mean" falsevalue="" checked="false" label="Mean depth" help="Report the mean depth of all positions in each A feature."/>
64 help="Positions reported are one based. Each position and depth follow the complete B feature" /> 62 <expand macro="overlap" name="overlap_a"/>
65 <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false" 63 <expand macro="overlap" name="overlap_b" argument="-F" fracof="B"/>
66 label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A" 64 <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Require that the fraction overlap be reciprocal for A AND B." 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"/>
67 help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" /> 65 <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Require that the minimum fraction be satisfied for A OR B." 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"/>
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 --> 66 <!-- -sorted -g -->
79 <expand macro="sorted" /> 67 <expand macro="sorted"/>
80 </inputs> 68 </inputs>
81 <outputs> 69 <outputs>
82 <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/> 70 <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
83 </outputs> 71 </outputs>
84 <tests> 72 <tests>
85 <test> 73 <test>
86 <param name="inputA" value="coverageBedA.bed" ftype="bed" /> 74 <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
87 <param name="inputB" value="coverageBedB.bed" ftype="bed" /> 75 <param name="reduce_or_iterate|inputB" value="coverageBedB.bed" ftype="bed"/>
88 <output name="output" file="coverageBed_result1.bed" ftype="bed" /> 76 <output name="output" file="coverageBed_result1.bed" ftype="bed"/>
89 </test> 77 </test>
90 <test> 78 <test>
91 <param name="inputA" value="multiCov1.bed" ftype="bed" /> 79 <param name="inputA" value="multiCov1.bed" ftype="bed"/>
92 <param name="inputB" value="srma_in3.bam" ftype="bam" /> 80 <param name="reduce_or_iterate|inputB" value="srma_in3.bam" ftype="bam"/>
93 <param name="sorted" value="true"/> 81 <param name="sorted" value="true"/>
94 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" /> 82 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>
95 </test> 83 </test>
96 <test> 84 <test>
97 <param name="inputA" value="multiCov1.bed" ftype="bed" /> 85 <param name="inputA" value="multiCov1.bed" ftype="bed"/>
98 <param name="reduce_or_iterate_selector" value="reduce" /> 86 <param name="reduce_or_iterate|reduce_or_iterate_selector" value="reduce"/>
99 <param name="inputB" value="srma_in3.bam" ftype="bam" /> 87 <param name="reduce_or_iterate|inputB" value="srma_in3.bam" ftype="bam"/>
100 <param name="sorted" value="true"/> 88 <param name="sorted" value="true"/>
101 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" /> 89 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>
102 </test> 90 </test>
103 <test> 91 <test>
104 <param name="inputA" value="coverageBedA.bed" ftype="bed" /> 92 <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
105 <param name="inputB" value="coverageBedB.bed" ftype="bed" /> 93 <param name="reduce_or_iterate|inputB" value="coverageBedB.bed" ftype="bed"/>
106 <param name="overlap_b" value="1" /> 94 <param name="overlap_b" value="1"/>
107 <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" /> 95 <output name="output" file="coverageBed_result2_F1.bed" ftype="bed"/>
108 </test> 96 </test>
109 <test> 97 <test>
110 <param name="inputA" value="coverageBedA.bed" ftype="bed" /> 98 <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
111 <param name="inputB" value="coverageBedB.bed" ftype="bed" /> 99 <param name="reduce_or_iterate|inputB" value="coverageBedB.bed" ftype="bed"/>
112 <param name="overlap_a" value="1E-5" /> 100 <param name="overlap_a" value="1E-5"/>
113 <param name="reciprocal_overlap" value="true" /> 101 <param name="reciprocal_overlap" value="true"/>
114 <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" /> 102 <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed"/>
115 </test> 103 </test>
116 <test> 104 <test>
117 <param name="inputA" value="multiCov1.bed" ftype="bed" /> 105 <param name="inputA" value="multiCov1.bed" ftype="bed"/>
118 <param name="reduce_or_iterate_selector" value="reduce" /> 106 <param name="reduce_or_iterate|reduce_or_iterate_selector" value="reduce"/>
119 <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" /> 107 <param name="reduce_or_iterate|inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam"/>
120 <param name="sorted" value="true"/> 108 <param name="sorted" value="true"/>
121 <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" /> 109 <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed"/>
122 </test> 110 </test>
123 <test> 111 <test>
124 <param name="inputA" value="coverageBedA2.bed" ftype="bed" /> 112 <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
125 <param name="inputB" value="coverageBed.bam" ftype="bam" /> 113 <param name="reduce_or_iterate|inputB" value="coverageBed.bam" ftype="bam"/>
126 <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" /> 114 <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed"/>
127 </test> 115 </test>
128 <test> 116 <test>
129 <param name="inputA" value="coverageBedA2.bed" ftype="bed" /> 117 <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
130 <param name="inputB" value="coverageBed.bam" ftype="bam" /> 118 <param name="reduce_or_iterate|inputB" value="coverageBed.bam" ftype="bam"/>
131 <param name="mean" value="true"/> 119 <param name="mean" value="true"/>
132 <output name="output" file="mean_coverage.bed" ftype="bed" /> 120 <output name="output" file="mean_coverage.bed" ftype="bed"/>
133 </test> 121 </test>
134 </tests> 122 </tests>
135 <help><![CDATA[ 123 <help><![CDATA[
136 **What it does** 124 **What it does**
137 125
153 3. The length of the entry in A. 141 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. 142 4. The fraction of bases in A that had non-zero coverage from features in B.
155 143
156 @REFERENCES@ 144 @REFERENCES@
157 ]]></help> 145 ]]></help>
158 <expand macro="citations" /> 146 <expand macro="citations"/>
159 </tool> 147 </tool>