# HG changeset patch
# User iuc
# Date 1630494255 0
# Node ID 3e38c9b3214f45d8e42a6ddac0da40b4905ba4f5
# Parent  fe5b4cb8356cbbdb6c85548e985cc7e488172ee8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"

diff -r fe5b4cb8356c -r 3e38c9b3214f annotateBed.xml
--- a/annotateBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/annotateBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@">
+<tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>annotate coverage of features from multiple files</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f bamToBed.xml
--- a/bamToBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/bamToBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1">
+<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>converter</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f bed12ToBed6.xml
--- a/bed12ToBed6.xml	Thu May 06 14:16:19 2021 +0000
+++ b/bed12ToBed6.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_bed12tobed6" name="bedtools BED12 to BED6" version="@TOOL_VERSION@">
+<tool id="bedtools_bed12tobed6" name="bedtools BED12 to BED6" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>converter</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f bedToBam.xml
--- a/bedToBam.xml	Thu May 06 14:16:19 2021 +0000
+++ b/bedToBam.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@">
+<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>converter</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f bedToIgv.xml
--- a/bedToIgv.xml	Thu May 06 14:16:19 2021 +0000
+++ b/bedToIgv.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@TOOL_VERSION@">
+<tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>create batch script for taking IGV screenshots</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f bedpeToBam.xml
--- a/bedpeToBam.xml	Thu May 06 14:16:19 2021 +0000
+++ b/bedpeToBam.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@">
+<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>converter</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f closestBed.xml
--- a/closestBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/closestBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@">
+<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>find the closest, potentially non-overlapping interval</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f clusterBed.xml
--- a/clusterBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/clusterBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@TOOL_VERSION@">
+<tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>cluster overlapping/nearby intervals</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f complementBed.xml
--- a/complementBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/complementBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@">
+<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>Extract intervals not represented by an interval file</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f coverageBed.xml
--- a/coverageBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/coverageBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@">
+<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>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f expandBed.xml
--- a/expandBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/expandBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_expandbed" name="bedtools ExpandBed" version="@TOOL_VERSION@">
+<tool id="bedtools_expandbed" name="bedtools ExpandBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>replicate lines based on lists of values in columns</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f fisherBed.xml
--- a/fisherBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/fisherBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@">
+<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>calculate Fisher statistic between two feature files</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f flankBed.xml
--- a/flankBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/flankBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@">
+<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>create new intervals from the flanks of existing intervals</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f genomeCoverageBed.xml
--- a/genomeCoverageBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/genomeCoverageBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@TOOL_VERSION@">
+<tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>compute the coverage over an entire genome</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f getfastaBed.xml
--- a/getfastaBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/getfastaBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@">
+<tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>use intervals to extract sequences from a FASTA file</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f groupbyBed.xml
--- a/groupbyBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/groupbyBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@">
+<tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>group by common cols and summarize other cols</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f intersectBed.xml
--- a/intersectBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/intersectBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@">
+<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>find overlapping intervals in various ways</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f jaccardBed.xml
--- a/jaccardBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/jaccardBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@">
+<tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>calculate the distribution of relative distances between two files</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f linksBed.xml
--- a/linksBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/linksBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_links" name="bedtools LinksBed" version="@TOOL_VERSION@">
+<tool id="bedtools_links" name="bedtools LinksBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>create a HTML page of links to UCSC locations</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f macros.xml
--- a/macros.xml	Thu May 06 14:16:19 2021 +0000
+++ b/macros.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -5,10 +5,16 @@
             <yield/>
         </requirements>
     </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">bedtools</xref>
+        </xrefs>
+    </xml>
     <token name="@TOOL_VERSION@">2.30.0</token>
     <token name="@SAMTOOLS_VERSION@">1.9</token>
     <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token>
     <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token>
+    <token name="@PROFILE@">20.05</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
diff -r fe5b4cb8356c -r 3e38c9b3214f makeWindowsBed.xml
--- a/makeWindowsBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/makeWindowsBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@">
+<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>make interval windows across a genome</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f mapBed.xml
--- a/mapBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/mapBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2">
+<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2" profile="@PROFILE@">
     <description>apply a function to a column for each overlapping interval</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f maskFastaBed.xml
--- a/maskFastaBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/maskFastaBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_maskfastabed" name="bedtools MaskFastaBed" version="@TOOL_VERSION@">
+<tool id="bedtools_maskfastabed" name="bedtools MaskFastaBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>use intervals to mask sequences from a FASTA file</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f mergeBed.xml
--- a/mergeBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/mergeBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@">
+<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>combine overlapping/nearby intervals into a single interval</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f multiCov.xml
--- a/multiCov.xml	Thu May 06 14:16:19 2021 +0000
+++ b/multiCov.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@">
+<tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>counts coverage from multiple BAMs at specific intervals</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f multiIntersectBed.xml
--- a/multiIntersectBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/multiIntersectBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@">
+<tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>identifies common intervals among multiple interval files</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f nucBed.xml
--- a/nucBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/nucBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_nucbed" name="bedtools NucBed" version="@TOOL_VERSION@">
+<tool id="bedtools_nucbed" name="bedtools NucBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>profile the nucleotide content of intervals in a FASTA file</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f overlapBed.xml
--- a/overlapBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/overlapBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@TOOL_VERSION@">
+<tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>computes the amount of overlap from two intervals</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f randomBed.xml
--- a/randomBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/randomBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@">
+<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>generate random intervals in a genome</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f reldist.xml
--- a/reldist.xml	Thu May 06 14:16:19 2021 +0000
+++ b/reldist.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_reldistbed" name="bedtools ReldistBed" version="@TOOL_VERSION@">
+<tool id="bedtools_reldistbed" name="bedtools ReldistBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>calculate the distribution of relative distances</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f shuffleBed.xml
--- a/shuffleBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/shuffleBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@">
+<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>randomly redistrubute intervals in a genome</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f slopBed.xml
--- a/slopBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/slopBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@">
+<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>adjust the size of intervals</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f sortBed.xml
--- a/sortBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/sortBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@">
+<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>order the intervals</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f spacingBed.xml
--- a/spacingBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/spacingBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_spacingbed" name="bedtools SpacingBed" version="@TOOL_VERSION@">
+<tool id="bedtools_spacingbed" name="bedtools SpacingBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>reports the distances between features</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f subtractBed.xml
--- a/subtractBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/subtractBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@TOOL_VERSION@">
+<tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>remove intervals based on overlaps</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f tagBed.xml
--- a/tagBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/tagBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@">
+<tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>tag BAM alignments based on overlaps with interval files</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f test-data/tagBed_result1.bam
Binary file test-data/tagBed_result1.bam has changed
diff -r fe5b4cb8356c -r 3e38c9b3214f unionBedGraphs.xml
--- a/unionBedGraphs.xml	Thu May 06 14:16:19 2021 +0000
+++ b/unionBedGraphs.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@TOOL_VERSION@">
+<tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>combines coverage intervals from multiple BEDGRAPH files</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r fe5b4cb8356c -r 3e38c9b3214f windowBed.xml
--- a/windowBed.xml	Thu May 06 14:16:19 2021 +0000
+++ b/windowBed.xml	Wed Sep 01 11:04:15 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bedtools_windowbed" name="bedtools WindowBed" version="@TOOL_VERSION@">
+<tool id="bedtools_windowbed" name="bedtools WindowBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>find overlapping intervals within a window around an interval</description>
+    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>