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comparison coverageBed.xml @ 63:7411007544bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit d1ee301a39e9830693eedb6ca089456081540f28
author iuc
date Thu, 02 Mar 2023 08:50:31 +0000
parents 539958feb49c
children f6c88d2e9ae5
comparison
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62:071c1c5d4bad 63:7411007544bf
1 <tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy1" 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" />
12 bedtools coverage 12 bedtools coverage
13 $d 13 $d
14 $hist 14 $hist
15 $split 15 $split
16 $strandedness 16 $strandedness
17 $mean
17 #if str($overlap_a): 18 #if str($overlap_a):
18 -f $overlap_a 19 -f $overlap_a
19 #end if 20 #end if
20 #if str($overlap_b): 21 #if str($overlap_b):
21 -F $overlap_b 22 -F $overlap_b
62 label="Report the depth at each position in each A feature" 63 label="Report the depth at each position in each A feature"
63 help="Positions reported are one based. Each position and depth follow the complete B feature" /> 64 help="Positions reported are one based. Each position and depth follow the complete B feature" />
64 <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false" 65 <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"
65 label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A" 66 label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
66 help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" /> 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."/>
67 <expand macro="overlap" name="overlap_a" /> 70 <expand macro="overlap" name="overlap_a" />
68 <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" /> 71 <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />
69 <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" 72 <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
70 label="Require that the fraction overlap be reciprocal for A AND B." 73 label="Require that the fraction overlap be reciprocal for A AND B."
71 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" /> 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" />
120 <test> 123 <test>
121 <param name="inputA" value="coverageBedA2.bed" ftype="bed" /> 124 <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
122 <param name="inputB" value="coverageBed.bam" ftype="bam" /> 125 <param name="inputB" value="coverageBed.bam" ftype="bam" />
123 <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" /> 126 <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
124 </test> 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>
125 </tests> 134 </tests>
126 <help><![CDATA[ 135 <help><![CDATA[
127 **What it does** 136 **What it does**
128 137
129 `bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in 138 `bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in