Mercurial > repos > pimarin > bedtools
diff coverageBed.xml @ 0:4cacc5b8001b draft default tip
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 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coverageBed.xml Thu Feb 23 09:50:24 2023 +0000 @@ -0,0 +1,159 @@ +<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@" profile="@PROFILE@"> + <description>of features in file B on the features in file A (bedtools coverage)</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools" /> + <expand macro="requirements"> + <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> + </expand> + <expand macro="stdio" /> + <command><![CDATA[ +bedtools coverage +$d +$hist +$split +$strandedness +$mean +#if str($overlap_a): + -f $overlap_a +#end if +#if str($overlap_b): + -F $overlap_b +#end if +$reciprocal_overlap +$a_or_b +-a '$inputA' +#if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate': + -b '$reduce_or_iterate.inputB' +#else: + -b + #for $file in $reduce_or_iterate.inputB + '$file' + #end for +#end if +@SORTED@ +#if $inputA.is_of_type('gff'): + | sort -k1,1 -k4,2n +#else: + | sort -k1,1 -k2,2n +#end if +> '$output' + ]]></command> + <inputs> + <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" /> + <conditional name="reduce_or_iterate"> + <param name="reduce_or_iterate_selector" type="select" label="Combined or separate output files"> + <option value="iterate" selected="true">One output file per 'input B' file</option> + <option value="reduce">Single output containing results for all 'input B' files</option> + </param> + <when value="iterate"> + <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"/> + </when> + <when value="reduce"> + <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true" + label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/> + </when> + </conditional> + <expand macro="split" /> + <param name="strandedness" argument="-s" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" + help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/> + <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" /> + <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" /> + <param name="mean" argument="-mean" type="boolean" label="Mean depth" truevalue="-mean" falsevalue="" checked="false" + help="Report the mean depth of all positions in each A feature."/> + <expand macro="overlap" name="overlap_a" /> + <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" /> + <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" /> + <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" /> + <!-- -sorted -g --> + <expand macro="sorted" /> + </inputs> + <outputs> + <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/> + </outputs> + <tests> + <test> + <param name="inputA" value="coverageBedA.bed" ftype="bed" /> + <param name="inputB" value="coverageBedB.bed" ftype="bed" /> + <output name="output" file="coverageBed_result1.bed" ftype="bed" /> + </test> + <test> + <param name="inputA" value="multiCov1.bed" ftype="bed" /> + <param name="inputB" value="srma_in3.bam" ftype="bam" /> + <param name="sorted" value="true"/> + <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" /> + </test> + <test> + <param name="inputA" value="multiCov1.bed" ftype="bed" /> + <param name="reduce_or_iterate_selector" value="reduce" /> + <param name="inputB" value="srma_in3.bam" ftype="bam" /> + <param name="sorted" value="true"/> + <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" /> + </test> + <test> + <param name="inputA" value="coverageBedA.bed" ftype="bed" /> + <param name="inputB" value="coverageBedB.bed" ftype="bed" /> + <param name="overlap_b" value="1" /> + <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" /> + </test> + <test> + <param name="inputA" value="coverageBedA.bed" ftype="bed" /> + <param name="inputB" value="coverageBedB.bed" ftype="bed" /> + <param name="overlap_a" value="1E-5" /> + <param name="reciprocal_overlap" value="true" /> + <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" /> + </test> + <test> + <param name="inputA" value="multiCov1.bed" ftype="bed" /> + <param name="reduce_or_iterate_selector" value="reduce" /> + <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" /> + <param name="sorted" value="true"/> + <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" /> + </test> + <test> + <param name="inputA" value="coverageBedA2.bed" ftype="bed" /> + <param name="inputB" value="coverageBed.bam" ftype="bam" /> + <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" /> + </test> + <test> + <param name="inputA" value="coverageBedA2.bed" ftype="bed" /> + <param name="inputB" value="coverageBed.bam" ftype="bam" /> + <param name="mean" value="true"/> + <output name="output" file="mean_coverage.bed" ftype="bed" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in +file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments +(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. +One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that +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. +Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A. + +.. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html + +.. class:: infomark + +The lines in the output will be comprised of each interval in A, followed by: + +1. The number of features in B that overlapped (by at least one base pair) the A interval. +2. The number of bases in A that had non-zero coverage from features in B. +3. The length of the entry in A. +4. The fraction of bases in A that had non-zero coverage from features in B. + +@REFERENCES@ + ]]></help> + <expand macro="citations" /> +</tool>