Mercurial > repos > iuc > bedtools
changeset 45:a1a923cd89e8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit d1ee301a39e9830693eedb6ca089456081540f28
| author | iuc |
|---|---|
| date | Thu, 02 Mar 2023 08:52:08 +0000 |
| parents | 589e7e57fd6d |
| children | |
| files | coverageBed.xml test-data/mean_coverage.bed |
| diffstat | 2 files changed, 13 insertions(+), 1 deletions(-) [+] |
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--- a/coverageBed.xml Mon Feb 20 21:49:48 2023 +0000 +++ b/coverageBed.xml Thu Mar 02 08:52:08 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@" profile="@PROFILE@"> +<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>of features in file B on the features in file A (bedtools coverage)</description> <macros> <import>macros.xml</import> @@ -14,6 +14,7 @@ $hist $split $strandedness +$mean #if str($overlap_a): -f $overlap_a #end if @@ -64,6 +65,8 @@ <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" @@ -122,6 +125,12 @@ <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**