--- a/coverageBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/coverageBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@">
+<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy1">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
@@ -7,87 +7,75 @@
         <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
     </expand>
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools coverage
-        $d
-        $hist
-        $split
-        $strandedness
-        #if str($overlap_a) != "None" and str($overlap_a):
-          -f '$overlap_a'
-        #end if
-        #if str($overlap_b) != "None" and str($overlap_b):
-          -F '$overlap_b'
-        #end if
-        $reciprocal_overlap
-        $a_or_b
-        -a '$inputA'
-        #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
-            -b '$reduce_or_iterate.inputB'
-            #if $reduce_or_iterate.inputB.is_of_type('bam'):
-                -sorted  -g <(samtools view -H $reduce_or_iterate.inputB | grep '^@SQ' |  sed $'s/\tSN:/\tSN\t/' | sed $'s/\tLN:/\tLN\t/' | cut -f 3,5)
-            #end if
-        #else:
-            #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
-            -b '$inputBs'
-        #end if
-        #if $inputA.is_of_type('gff') or $inputA.is_of_type('gff3'):
-            | sort -k1,1 -k4,2n
-        #else:
-            | sort -k1,1 -k2,2n
-        #end if
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools coverage
+$d
+$hist
+$split
+$strandedness
+#if str($overlap_a):
+    -f $overlap_a
+#end if
+#if str($overlap_b):
+    -F $overlap_b
+#end if
+$reciprocal_overlap
+$a_or_b
+-a '$inputA'
+#if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
+    -b '$reduce_or_iterate.inputB'
+    #if $reduce_or_iterate.inputB.is_of_type('bam'):
+        -sorted -g <(samtools view -H $reduce_or_iterate.inputB | grep '^@SQ' |  sed $'s/\tSN:/\tSN\t/' | sed $'s/\tLN:/\tLN\t/' | cut -f 3,5)
+    #end if
+#else:
+    -b
+    #for $file in $reduce_or_iterate.inputB
+        '$file'
+    #end for
+#end if
+#if $inputA.is_of_type('gff'):
+    | sort -k1,1 -k4,2n
+#else:
+    | sort -k1,1 -k2,2n
+#end if
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
+        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ 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 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,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data"
-                       label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
+            <when value="iterate">
+                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@"
+                       label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
             </when>
-            <when value='reduce'>
-                <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" multiple="true"
+            <when value="reduce">
+                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true"
                        label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ 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)"/>
-        <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
+        <param name="strandedness" argument="-s" 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"/>
+        <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
             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=""
+            help="Positions reported are one based. Each position and depth follow the complete B feature" />
+        <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"
             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)" />
-        <param name="overlap_a" type="text"
-            label="Minimum overlap required as a fraction of A."
-            help="Default is 1E-9 (i.e., 1bp). (-f)">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value=",."/></valid>
-            </sanitizer>
-        </param>
-        <param name="overlap_b" type="text"
-            label="Minimum overlap required as a fraction of B."
-            help="Default is 1E-9 (i.e., 1bp). (-F)">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value=",."/></valid>
-            </sanitizer>
-        </param>
-        <param name="reciprocal_overlap" type="boolean" checked="false" truevalue="-r" falsevalue=""
+            help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" />
+        <expand macro="overlap" name="overlap_a" />
+        <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />
+        <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
             label="Require that the fraction overlap be reciprocal for A AND B."
-            help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B (-r)" />
-        <param name="a_or_b" type="boolean" checked="false" truevalue="-e" falsevalue=""
+            help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B" />
+        <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
             label="Require that the minimum fraction be satisfied for A OR B."
-            help="if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of  B is covered. Without -e, both fractions would have to be satisfied. (-e)" />
+            help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of  B is covered. Without -e, both fractions would have to be satisfied" />
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
+        <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
     </outputs>
     <tests>
         <test>
@@ -115,13 +103,12 @@
         <test>
             <param name="inputA" value="coverageBedA.bed" ftype="bed" />
             <param name="inputB" value="coverageBedB.bed" ftype="bed" />
-            <param name="overlap_a" value="1"  />
+            <param name="overlap_a" value="1E-5"  />
             <param name="reciprocal_overlap" value="true"  />
             <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 `bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in
@@ -143,7 +130,6 @@
 4. The fraction of bases in A that had non-zero coverage from features in B.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>