# HG changeset patch
# User iuc
# Date 1677747031 0
# Node ID 7411007544bf90d426cf08e0021e3ddd8547e6f0
# Parent  071c1c5d4badc0ff7975a6aff57321e736b3a51b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit d1ee301a39e9830693eedb6ca089456081540f28

diff -r 071c1c5d4bad -r 7411007544bf coverageBed.xml
--- a/coverageBed.xml	Mon Feb 20 21:48:16 2023 +0000
+++ b/coverageBed.xml	Thu Mar 02 08:50:31 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**
diff -r 071c1c5d4bad -r 7411007544bf test-data/mean_coverage.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mean_coverage.bed	Thu Mar 02 08:50:31 2023 +0000
@@ -0,0 +1,3 @@
+dummy_chr	1	100	0.0000000
+dummy_chr	1000	1000000	0.0001522
+super_dummy_chr	1	100	0.0000000