# HG changeset patch
# User iuc
# Date 1515630093 18000
# Node ID df56e1b12d0c1c70ee536a073534d691116f3369
# Parent  a8eabd2838f6deb7ce8ae879b553496ffa69a3f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a

diff -r a8eabd2838f6 -r df56e1b12d0c coverageBed.xml
--- a/coverageBed.xml	Fri Dec 08 03:26:42 2017 -0500
+++ b/coverageBed.xml	Wed Jan 10 19:21:33 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
@@ -7,8 +7,6 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        #set inputBs = "' '".join([str($file) for $file in $inputB])
-
         bedtools coverage
         $d
         $hist
@@ -23,14 +21,32 @@
         $reciprocal_overlap
         $a_or_b
         -a '$inputA'
-        -b '$inputBs'
+        #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
+            -b '$reduce_or_iterate.inputB'
+        #else:
+            #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
+            -b '$inputBs'
+        #end if
         | sort -k1,1 -k2,2n
         > '$output'
 ]]>
     </command>
     <inputs>
         <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" />
+        <conditional name="reduce_or_iterate">
+            <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
+                <option value='iterate' selected='true'>One output file per 'input B' file</option>
+                <option value='reduce'>Single output containing results for all 'input B' files</option>
+            </param>
+            <when value='iterate'>
+                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data"
+                       label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/>
+            </when>
+            <when value='reduce'>
+                <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"/>
+            </when>
+        </conditional>
         <expand macro="split" />
         <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
             help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>
diff -r a8eabd2838f6 -r df56e1b12d0c intersectBed.xml
--- a/intersectBed.xml	Fri Dec 08 03:26:42 2017 -0500
+++ b/intersectBed.xml	Wed Jan 10 19:21:33 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_intersectbed" name="Intersect intervals" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_intersectbed" name="Intersect intervals" version="@WRAPPER_VERSION@.1">
     <description>find overlapping intervals in various ways</description>
     <macros>
         <import>macros.xml</import>
@@ -7,21 +7,25 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        #set inputBs = '" "'.join( [ str( $file ) for $file in $inputB ] )
         #set modes = ' '.join( str($overlap_mode).split(',') )
 
         bedtools intersect
             #if $inputA.is_of_type('bam'):
-                -abam "${inputA}"
+                -abam '${inputA}'
             #else:
-                -a "${inputA}"
+                -a '${inputA}'
             #end if
 
-            -b "${inputBs}"
+            #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
+                -b '$reduce_or_iterate.inputB'
+            #else:
+                #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
+                -b '$inputBs'
+            #end if
             $split
             $strand
             #if str($fraction) != "None" and str($fraction):
-              -f "${fraction}"
+              -f '${fraction}'
             #end if
             $reciprocal
             $invert
@@ -29,12 +33,25 @@
             $header
             $modes
             $count
-            > "${output}"
+            > '${output}'
 ]]>
     </command>
     <inputs>
-        <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
-        <param format="bed,bam,gff,vcf,gff3" name="inputB" type="data" multiple="True" label="One or more BAM/BED/GFF/VCF file(s)"/>
+        <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="File A to intersect with B" help="BAM/BED/GFF/VCF format" />
+        <conditional name="reduce_or_iterate">
+            <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
+                <option value='iterate' selected='true'>One output file per 'input B' file</option>
+                <option value='reduce'>Single output containing intersections of any 'input B' lines with A </option>
+            </param>
+            <when value='iterate'>
+                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data"
+                       label="File(s) B to intersect with A" help="BAM/BED/GFF/VCF format"/>
+            </when>
+            <when value='reduce'>
+                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true"
+                       label="File(s) B to intersect with A" help="BAM/BED/GFF/VCF format"/>
+            </when>
+        </conditional>
         <expand macro="strand2" />
         <param name="overlap_mode" type="select" multiple="True" label="What should be written to the output file?">
             <option value="-wa" selected="True">Write the original entry in A for each overlap (-wa)</option>
@@ -53,7 +70,7 @@
         <expand macro="reciprocal" />
         <!-- -v -->
         <param name="invert" type="boolean" checked="false" truevalue="-v" falsevalue=""
-            label="Report only those alignments that **do not** overlap the BED file"
+            label="Report only those alignments that **do not** overlap with file(s) B"
             help="(-v)"/>
         <!-- -u -->
         <param name="once" type="boolean" checked="false" truevalue="-u" falsevalue=""