| Previous changeset 38:fe5b4cb8356c (2021-05-06) Next changeset 40:a68aa6c1204a (2021-09-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2" |
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modified:
annotateBed.xml bamToBed.xml bed12ToBed6.xml bedToBam.xml bedToIgv.xml bedpeToBam.xml closestBed.xml clusterBed.xml complementBed.xml coverageBed.xml expandBed.xml fisherBed.xml flankBed.xml genomeCoverageBed.xml getfastaBed.xml groupbyBed.xml intersectBed.xml jaccardBed.xml linksBed.xml macros.xml makeWindowsBed.xml mapBed.xml maskFastaBed.xml mergeBed.xml multiCov.xml multiIntersectBed.xml nucBed.xml overlapBed.xml randomBed.xml reldist.xml shuffleBed.xml slopBed.xml sortBed.xml spacingBed.xml subtractBed.xml tagBed.xml test-data/tagBed_result1.bam unionBedGraphs.xml windowBed.xml |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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 --> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| diff -r fe5b4cb8356c -r 3e38c9b3214f test-data/tagBed_result1.bam |
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| Binary file test-data/tagBed_result1.bam has changed |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |