Mercurial > repos > iuc > bedtools

changeset 39:3e38c9b3214f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
author iuc
date Wed, 01 Sep 2021 11:04:15 +0000
parents fe5b4cb8356c
children a68aa6c1204a
files 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
diffstat 39 files changed, 80 insertions(+), 37 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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 -->
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
Binary file test-data/tagBed_result1.bam has changed
--- 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>
--- 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>