# HG changeset patch
# User iuc
# Date 1463934812 14400
# Node ID d25966c8ddeb1827ab46255b99bc3ef000332e62
# Parent  f8b7dc21b4eee6bf7d79b7d84b1e8b3d8561430a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f-dirty

diff -r f8b7dc21b4ee -r d25966c8ddeb closestBed.xml
--- a/closestBed.xml	Sat Feb 27 12:56:56 2016 -0500
+++ b/closestBed.xml	Sun May 22 12:33:32 2016 -0400
@@ -7,7 +7,7 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        #set inputBs = ' '.join( [ str( $file ) for $file in $inputB ] )
+        #set inputBs = "' '".join([str( $file ) for $file in $inputB])
 
         closestBed
         $strand
@@ -23,8 +23,8 @@
         #if $k:
             -k $k
         #end if
-        -a $inputA
-        -b $inputBs
+        -a '$inputA'
+        -b '$inputBs'
         > $output
 ]]>
     </command>
diff -r f8b7dc21b4ee -r d25966c8ddeb coverageBed.xml
--- a/coverageBed.xml	Sat Feb 27 12:56:56 2016 -0500
+++ b/coverageBed.xml	Sun May 22 12:33:32 2016 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
-    <description>of features in file A across the features in file B (coverageBed)</description>
+    <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -7,36 +7,34 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        coverageBed
-        #if $inputA.ext == "bam"
-            -abam '$inputA'
-        #else
-            -a '$inputA'
-        #end if
-        -b '$inputB'
+        #set inputBs = "' '".join([str($file) for $file in $inputB])
+
+        bedtools coverage
         $d
         $hist
         $split
         $strandedness
+        -a '$inputA'
+        -b '$inputBs'
         | sort -k1,1 -k2,2n
         > '$output'
 ]]>
     </command>
     <inputs>
-        <param format="bed,bam,gff,gg3,vcf" name="inputA" type="data" label="Count how many intervals in this BED/VCF/GFF/BAM file (source)" />
-        <param format="bed,gff,gff3,vcf" name="inputB" type="data" label="overlap the intervals in this BED file (target)" />
+        <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
+        <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
         <expand macro="split" />
         <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 
-            help="That is, only features in A are only counted towards coverage in B if they are the same strand. (-s)"/>
+            help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>
         <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
-            label="Report the depth at each position in each B feature"
-            help="Positions reported are one based.  Each position and depth follow the complete B feature. (-d)" />
+            label="Report the depth at each position in each A feature"
+            help="Positions reported are one based. Each position and depth follow the complete B feature (-d)" />
         <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""
-            label="Report a histogram of coverage for each feature in B as well as a summary histogram for all features in B"
-            help="Additonal columns after each feature in B: 1) depth 2) # bases at depth 3) size of B 4) % of B at depth. (-hist)" />
+            label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
+            help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth (-hist)" />
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="inputB" label="Count of overlaps in ${inputA.name} on ${inputB.name}"/>
+        <data format="bed" name="output" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
     </outputs>
     <tests>
         <test>
@@ -49,18 +47,23 @@
 <![CDATA[
 **What it does**
 
-coverageBed_ computes both the depth and breadth of coverage of features in 
-file A across the features in file B. For example, coverageBed can compute the coverage of sequence alignments 
-(file A) across 1 kilobase (arbitrary) windows (file B) tiling a genome of interest. 
-One advantage that coverageBed offers is that it not only counts the number of features that 
-overlap an interval in file B, it also computes the fraction of bases in B interval that were overlapped by one or more features.
-Thus, coverageBed also computes the breadth of coverage for each interval in B.
+`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in 
+file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments 
+(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. 
+One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that 
+overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features.
+Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.
 
-.. _coverageBed: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
+.. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
 
 .. class:: infomark
 
-The output file will be comprised of each interval from your original target BED file, plus an additional column indicating the number of intervals in your source file that overlapped that target interval.
+The lines in the output will be comprised of each interval in A, followed by:
+
+1. The number of features in B that overlapped (by at least one base pair) the A interval.
+2. The number of bases in A that had non-zero coverage from features in B.
+3. The length of the entry in A.
+4. The fraction of bases in A that had non-zero coverage from features in B.
 
 @REFERENCES@
 ]]>
diff -r f8b7dc21b4ee -r d25966c8ddeb shuffleBed.xml
--- a/shuffleBed.xml	Sat Feb 27 12:56:56 2016 -0500
+++ b/shuffleBed.xml	Sun May 22 12:33:32 2016 -0400
@@ -15,10 +15,10 @@
             -seed $seed.seed
         #end if
         #if str($add_bed.add_bed_select) == "not_be":
-            -excl $add_bed_select.excl
-            -f $add_bed_select.overlap
+            -excl $add_bed.excl
+            -f $add_bed.overlap
         #elif str($add_bed.add_bed_select) == "be":
-            -incl $add_bed_select.incl
+            -incl $add_bed.incl
         #end if
         $chrom
         $chromfirst