Mercurial > repos > iuc > bedtools

changeset 57:1d0a0d6a78b1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
author iuc
date Wed, 01 Sep 2021 11:02:26 +0000
parents 7a06bb42dbb1
children ed6f66aed1f9
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 macros.xml.orig 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 40 files changed, 38 insertions(+), 325 deletions(-) [+]
line wrap: on
line diff
--- a/annotateBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/annotateBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/bamToBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/bamToBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/bed12ToBed6.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/bed12ToBed6.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/bedToBam.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/bedToBam.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/bedToIgv.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/bedToIgv.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/bedpeToBam.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/bedpeToBam.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/closestBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/closestBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/clusterBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/clusterBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/complementBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/complementBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/coverageBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/coverageBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/expandBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/expandBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/fisherBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/fisherBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/flankBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/flankBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/genomeCoverageBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/genomeCoverageBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/getfastaBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/getfastaBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/groupbyBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/groupbyBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/intersectBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/intersectBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/jaccardBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/jaccardBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/linksBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/linksBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/macros.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/macros.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -14,6 +14,7 @@
     <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/macros.xml.orig	Tue Aug 31 07:45:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,288 +0,0 @@
-<macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="@TOOL_VERSION@">bedtools</requirement>
-            <yield/>
-        </requirements>
-    </xml>
-<<<<<<< HEAD
-    <token name="@TOOL_VERSION@">2.30.0</token>
-=======
-    <xml name="bio_tools">
-        <xrefs>
-            <xref type='bio.tools'>bedtools</xref>
-        </xrefs>
-    </xml>
-    <token name="@TOOL_VERSION@">2.29.2</token>
->>>>>>> 405b19246 (add bio.tool ID)
-    <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>
-    <xml name="stdio">
-        <stdio>
-            <!-- Anything other than zero is an error -->
-            <exit_code range="1:" />
-            <exit_code range=":-1" />
-            <!-- In case the return code has not been set propery check stderr too -->
-            <regex match="Error:" />
-            <regex match="Exception:" />
-        </stdio>
-        <version_command>bedtools --version</version_command>
-    </xml>
-    <xml name="reciprocal">
-        <param name="reciprocal" argument="-r" type="select" label="Require that the fraction of overlap be reciprocal for A and B" help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.">
-            <option value="" selected="true">No</option>
-            <option value="-r">Yes</option>
-        </param>
-    </xml>
-    <xml name="fraction" token_name="" token_argument="" token_label="" token_help="" >
-        <param name="@NAME@" argument="@ARGUMENT@" type="float" min="0" max="1" optional="true" label="@LABEL@" help="@HELP@" />
-    </xml>
-    <xml name="overlap" token_name="overlap" token_argument="-f" token_fracof="A">
-        <expand macro="fraction" name="@NAME@" argument="@ARGUMENT@" label="Minimum overlap required as a fraction of @FRACOF@" help="Default is 1E-9, i.e. 1bp."/>
-    </xml>
-    <token name="@OVERLAP@"><![CDATA[
-        #if str($overlap):
-            -f $overlap
-        #end if
-    ]]></token>
-    <xml name="strand2">
-        <param name="strand" type="select" label="Calculation based on strandedness?">
-            <option value="" selected="true">Overlaps on either strand</option>
-            <option value="-s">Only overlaps occurring on the **same** strand.</option>
-            <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
-        </param>
-    </xml>
-    <xml name="seed">
-        <conditional name="seed">
-            <param name="seed_choose" type="select" label="Choose Seed?">
-                <option value="False" selected="true">Random Shuffling</option>
-                <option value="True">Choose fixed seed</option>
-            </param>
-            <when value="True">
-                <param argument="-seed" type="integer" value="12345" label="Enter Seed" />
-            </when>
-            <when value="False" />
-        </conditional>
-    </xml>
-    <xml name="split">
-        <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false"
-            label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
-            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
-    </xml>
-    <xml name="input_conditional_genome_file">
-        <conditional name="genome_file_opts">
-            <param name="genome_file_opts_selector" type="select" label="Genome file">
-                <option value="loc" selected="true">Locally installed Genome file</option>
-                <option value="hist">Genome file from your history</option>
-            </param>
-            <when value="loc">
-                <param name="genome" type="select" multiple="false" label="Genome file">
-                    <options from_data_table="__dbkeys__" />
-                </param>
-            </when>
-            <when value="hist">
-                <param name="genome" type="data" format="tabular" label="Genome file" />
-            </when>
-        </conditional>
-    </xml>
-    <xml name="input_optional_genome_file">
-        <conditional name="genome">
-            <param name="genome_choose" argument="-g" type="select"
-                label="Specify a genome file that defines the expected chromosome order in the input files." >
-                <option value="" selected="true">No</option>
-                <option value="-g">Yes</option>
-            </param>
-            <when value="-g">
-                <expand macro="input_conditional_genome_file" />
-            </when>
-            <when value="" />
-        </conditional>
-    </xml>
-    <token name="@GENOME_FILE@">
-#if $genome_file_opts.genome_file_opts_selector == "loc":
-    '$genome_file_opts.genome.fields.len_path'
-#elif $genome_file_opts.genome_file_opts_selector == "hist":
-    '$genome_file_opts.genome'
-#end if
-    </token>
-    <token name="@GENOME_FILE_MAPBED@">
-#if $genome.genome_choose == "-g":
-    #if $genome.genome_file_opts.genome_file_opts_selector == "loc":
-        -g '$genome.genome_file_opts.genome.fields.len_path'
-    #elif $genome.genome_file_opts.genome_file_opts_selector == "hist":
-        -g '$genome.genome_file_opts.genome'
-    #end if
-#end if
-    </token>
-    <token name="@GENOME_FILE_MAKEWINDOWS@">
-#if $type.type_select == "genome":
-    #if $type.genome_file_opts.genome_file_opts_selector == "loc":
-        -g '$type.genome_file_opts.genome.fields.len_path'
-    #elif $type.genome_file_opts.genome_file_opts_selector == "hist":
-        -g '$type.genome_file_opts.genome'
-    #end if
-#end if
-    </token>
-    <token name="@GENOME_FILE_UNION@">
-#if $empty.empty_selector == "-empty":
-    #if $empty.genome_file_opts.genome_file_opts_selector == "loc":
-        -g '$empty.genome_file_opts.genome.fields.len_path'
-    #elif $empty.genome_file_opts.genome_file_opts_selector == "hist":
-        -g '$empty.genome_file_opts.genome'
-    #end if
-#end if
-    </token>
-    <token name="@GENOME_FILE_COVERAGE@">
-#if $input_type.input_type_select == "bam":
-    -ibam '$input_type.input'
-#else:
-    -i '$input_type.input'
-    #if $input_type.genome_file_opts.genome_file_opts_selector == "loc":
-        -g '$input_type.genome_file_opts.genome.fields.len_path'
-    #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist":
-        -g '$input_type.genome_file_opts.genome'
-    #end if
-#end if
-    </token>
-    <xml name="closest_D_option">
-        <param argument="-iu" type="boolean" truevalue="-iu" falsevalue="" checked="false"
-            label="Ignore features in B that are upstream of features in A"
-            help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
-
-        <param argument="-id" type="boolean" truevalue="-id" falsevalue="" checked="false"
-            label="Ignore features in B that are downstream of features in A"
-            help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
-
-        <param argument="-fu" type="boolean" truevalue="-fu" falsevalue="" checked="false"
-            label="Choose first from features in B that are upstream of features in A"
-            help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
-
-        <param argument="-fd" type="boolean" truevalue="-fd" falsevalue="" checked="false"
-            label="Choose first from features in B that are downstream of features in A"
-            help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
-    </xml>
-    <xml name="addition">
-        <conditional name="addition">
-            <param name="addition_select" type="select" label="Choose what you want to do">
-                <option value="b" selected="true">Increase the @STD_BEDTOOLS_INPUT_LABEL@ entry by the same number base pairs in each direction.</option>
-                <option value="lr">Increase by Start Coordinate and End Coordinate</option>
-            </param>
-            <when value="b">
-                <param name="b" value="1" label="Number of base pairs" type="integer" />
-            </when>
-            <when value="lr">
-                <param name="l" type="integer" value="0" label="The number of base pairs to subtract from the start coordinate" />
-                <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" />
-            </when>
-        </conditional>
-    </xml>
-    <xml name="print_header">
-        <param argument="-header" type="boolean" truevalue="-header" falsevalue="" checked="false"
-            label="Print the header from the A file prior to results" />
-    </xml>
-    <!-- TODO this is currently not used, but we should make use of it -->
-    <xml name="genome_validator">
-        <validator type="unspecified_build" />
-        <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
-    </xml>
-
-    <!-- ToDo column_picker -->
-    <xml name="choose_columns">
-        <param name="cols" argument="-c" type="text" value=""
-            label="Specify the column(s) that should be summarized"
-            help="Comma separated">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value=","/></valid>
-            </sanitizer>
-        </param>
-    </xml>
-
-    <token name="@C_AND_O_ARGUMENT@">
-        #set $col = list()
-        #set $op = list()
-        #for $item in $c_and_o_argument_repeat:
-            #silent $col.append( str($item.col) )
-            #silent $op.append( str($item.operation) )
-        #end for
-        #if $col:
-            -c #echo ','.join($col)#
-            -o #echo ','.join($op)#
-        #end if
-    </token>
-
-    <xml name="c_and_o_argument">
-        <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0">
-            <yield />
-            <expand macro="choose_operations">
-                <expand macro="math_options" />
-                <expand macro="additional_math_options" />
-            </expand>
-        </repeat>
-    </xml>
-
-    <xml name="choose_operations">
-        <param name="operation" type="select" label="Specify the operation">
-            <yield />
-        </param>
-    </xml>
-
-    <xml name="math_options">
-        <option value="sum" selected="true">Sum - numeric only</option>
-        <option value="min">Min - numeric only</option>
-        <option value="max">Max - numeric only</option>
-        <option value="absmin">AbsMin - numeric only</option>
-        <option value="absmax">AbsMax - numeric only</option>
-        <option value="mean">Mean - numeric only</option>
-        <option value="median">Median - numeric only</option>
-        <option value="mode">Mode - numeric only</option>
-        <option value="antimode">Antimode - numeric only</option>
-        <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
-    </xml>
-    <xml name="additional_math_options">
-        <option value="count">Count - numeric or text</option>
-        <option value="count_disctinct">Count Distinct - numeric or text</option>
-        <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
-        <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
-    </xml>
-    <xml name="sorted">
-        <!-- -sorted -g  -->
-        <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
-            label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/>
-    </xml>
-    <token name="@SORTED@">
-<![CDATA[
-$sorted
-#if str($sorted) != '':
-    #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
-        -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
-    #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
-        -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
-    #end if
-#end if
-]]>
-    </token>
-    <token name="@REFERENCES@">
-<![CDATA[
-------
-
-This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.
-
-.. _bedtools package: https://github.com/arq5x/bedtools2
-.. _Quinlan laboratory: http://quinlanlab.org
-
-
-**Citation**
-
-If you use this tool in Galaxy, please cite:
-
-Bjoern A. Gruening (2014), `Galaxy wrapper <https://github.com/bgruening/galaxytools>`_
-]]>
-    </token>
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1093/bioinformatics/btq033</citation>
-            <yield />
-        </citations>
-    </xml>
-</macros>
--- a/makeWindowsBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/makeWindowsBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/mapBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/mapBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/maskFastaBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/maskFastaBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/mergeBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/mergeBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/multiCov.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/multiCov.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/multiIntersectBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/multiIntersectBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/nucBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/nucBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/overlapBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/overlapBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/randomBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/randomBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/reldist.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/reldist.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/shuffleBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/shuffleBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/slopBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/slopBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/sortBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/sortBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/spacingBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/spacingBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/subtractBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/subtractBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/tagBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/tagBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
Binary file test-data/tagBed_result1.bam has changed
--- a/unionBedGraphs.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/unionBedGraphs.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>
--- a/windowBed.xml	Tue Aug 31 07:45:56 2021 +0000
+++ b/windowBed.xml	Wed Sep 01 11:02:26 2021 +0000
@@ -1,4 +1,4 @@
-<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>