# HG changeset patch
# User iuc
# Date 1556531748 14400
# Node ID dde39ba9c03186fa5c0f63101a33d694775028d3
# Parent  87ee588b3d453e0b9531b5dbe76e5fb613a0393b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

diff -r 87ee588b3d45 -r dde39ba9c031 annotateBed.xml
--- a/annotateBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/annotateBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,65 +1,65 @@
-<tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@+galaxy1">
     <description>annotate coverage of features from multiple files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-
-        bedtools annotate
-        -i "${inputA}"
-        #if $names.names_select == 'yes':
-            -files
-            #for $bed in $names.beds:
-                "${bed.input}"
-            #end for
+    <command><![CDATA[
+bedtools annotate
+-i '${inputA}'
+#if $names.names_select == 'yes':
+    -files
+    #for $bed in $names.beds:
+        '${bed.input}'
+    #end for
 
-            -names
-            #for $bed in $names.beds:
-                "${bed.inputName}"
-            #end for
-        #else:
-            #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
-            -files "${files}"
-            #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] )
-            -names "${names}"
-        #end if
-        $strand
-        $counts
-        $both
-        > "${output}"
-]]>
-    </command>
+    -names
+    #for $bed in $names.beds:
+        '${bed.inputName}'
+    #end for
+#else:
+    -files
+    #for $bed in $names.beds:
+        '$bed'
+    #end for
+    -names
+    #for $bed in $names.beds:
+        '${bed.display_name}'
+    #end for
+#end if
+$strand
+$counts
+$both
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
-        <!-- Additional files, if the user needs more -->
-         <conditional name="names">
+        <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
+        <conditional name="names">
             <param name="names_select" type="select" label="Specify names for each file">
-                <option value="no" selected="True">No</option>
+                <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="yes">
                 <repeat name="beds" title="Add BED files and names" >
-                    <param name="input" format="bed" type="data" label="BED file" />
+                    <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
                     <param name="inputName" type="text" label="Name of the file" />
                 </repeat>
             </when>
             <when value="no">
-                <param name="beds" format="bed" multiple="True" type="data" label="BED file" />
+                <param name="beds" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
             </when>
         </conditional>
         <expand macro="strand2" />
-        <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue=""
+        <param argument="-counts" type="boolean" truevalue="-counts" falsevalue="" checked="false"
             label="Report the count of features followed by the % coverage for each annotation file"
-            help="Default is to report solely the fraction of -i covered by each file." />
-        <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue=""
+            help="Default is to report solely the fraction of -i covered by each file" />
+        <param argument="-both" type="boolean" truevalue="-both" falsevalue="" checked="false"
             label="Report the count of features followed by the % coverage for each annotation file"
-            help="Default is to report solely the fraction of the input file covered by each file." />
+            help="Default is to report solely the fraction of the input file covered by each file" />
     </inputs>
     <outputs>
-        <data format="bed" name="output" />
+        <data name="output" format="bed" />
     </outputs>
     <tests>
         <test>
@@ -69,14 +69,12 @@
             <output name="output" file="annotateBed_result.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools annotate, well, annotates one @STD_BEDTOOLS_INPUT_LABEL@ file with the coverage and number of overlaps observed from multiple other @STD_BEDTOOLS_INPUT_LABEL@ files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 bamToBed.xml
--- a/bamToBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bamToBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -7,41 +7,38 @@
         <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
     </expand>
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-
-        #if $input.extension == 'bam' and $option == "-bedpe":
-            samtools sort -n "${input}" ./input &&
-        #else
-            ln -s "${input}" ./input.bam &&
-        #end if
+    <command><![CDATA[
+#if $input.extension == 'bam' and $option == "-bedpe":
+    samtools sort -n '${input}' ./input &&
+#else
+    ln -s '${input}' ./input.bam &&
+#end if
 
-        bedtools bamtobed
-        $option
-        $ed_score
-        $split
-        #if $tag and str($tag).strip():
-          -tag "${tag}"
-        #end if
-        -i ./input.bam
-        > "${output}"
-]]>
-    </command>
+bedtools bamtobed
+$option
+$ed_score
+$split
+#if $tag and str($tag).strip():
+    -tag '${tag}'
+#end if
+-i ./input.bam
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
+        <param name="input" type="data" format="bam" label="Convert the following BAM file to BED"/>
         <param name="option" type="select" label="What type of BED output would you like">
             <option value="">Create a 6-column BED file</option>
             <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
             <option value="-bedpe">Create a paired-end, BEDPE format</option>
         </param>
         <expand macro="split" />
-        <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false"
-            label="Use alignment's edit-distance for BED score" help="(-ed)" />
-        <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"
-            help="(-tag)"/>
+        <param name="ed_score" argument="-ed" type="boolean" truevalue="-ed" falsevalue="" checked="false"
+            label="Use alignment's edit-distance for BED score" />
+        <param argument="-tag" type="text" optional="true"
+            label="Use other NUMERIC BAM alignment tag as the BED score" />
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
+        <data name="output" format="bed" metadata_source="input" label="${input.name} (as BED)"/>
     </outputs>
     <tests>
         <test>
@@ -57,8 +54,7 @@
             <output name="output" file="bamToBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
@@ -77,7 +73,6 @@
 
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 bamToFastq.xml
--- a/bamToFastq.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bamToFastq.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,28 +1,28 @@
-<tool id="bedtools_bamtofastq" name="bedtools Convert from BAM to FastQ" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bamtofastq" name="bedtools Convert from BAM to FastQ" version="@TOOL_VERSION@">
     <description></description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-        bedtools bamtofastq
-        $tags
-        -i '$input'
-        -fq '$output'
-        #if $fq2:
-           -fq2 '$output2'
-        #end if
-    </command>
+    <command><![CDATA[
+bedtools bamtofastq
+$tags
+-i '$input'
+-fq '$output'
+#if $fq2:
+    -fq2 '$output2'
+#end if
+    ]]></command>
     <inputs>
-        <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
-        <param name="tags" type="boolean" truevalue="-tags" falsevalue="" checked="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
-        <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="False" label="FASTQ for second end.
-            Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
+        <param name="input" type="data" format="bam" label="Convert the following BAM file to FASTQ"/>
+        <param argument="-tags" type="boolean" truevalue="-tags" falsevalue="" checked="false" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
+        <param argument="-fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="false" label="FASTQ for second end"
+            help="Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
     </inputs>
     <outputs>
-        <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
-        <data format="fastq" name="output2" metadata_source="input" label="${input.name} (as FASTQ)">
+        <data name="output" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)"/>
+        <data name="output2" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)">
             <filter>fq2 is True</filter>
         </data>
     </outputs>
@@ -32,14 +32,12 @@
             <output name="output" file="bamToFastq_result1.fastq" ftype="fastq" />
         </test>
     </tests>
-<help>
-
+    <help><![CDATA[
 **What it does**
 
 bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
 
 @REFERENCES@
-
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 bed12ToBed6.xml
--- a/bed12ToBed6.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bed12ToBed6.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,22 +1,20 @@
-<tool id="bedtools_bed12tobed6" name="bedtools BED12 to BED6" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bed12tobed6" name="bedtools BED12 to BED6" version="@TOOL_VERSION@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bed12ToBed6
-        -i '$input'
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bed12ToBed6
+-i '$input'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bed" name="input" type="data" label="Convert the following BED12 file to BED6"/>
+        <param name="input" argument="-i" type="data" format="bed" label="Convert the following BED12 file to BED6"/>
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED6)"/>
+        <data name="output" format="bed" metadata_source="input" label="${input.name} (as BED6)"/>
     </outputs>
     <tests>
         <test>
@@ -24,14 +22,12 @@
             <output name="output" file="bed12ToBed6_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bed12ToBed6 is a convenience tool that converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to discrete BED6 features. For example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 bedToBam.xml
--- a/bedToBam.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bedToBam.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,31 +1,29 @@
-<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools bedtobam
-        $bed12
-        -mapq $mapq
-        -g @GENOME_FILE@
-        -i '$input'
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools bedtobam
+$bed12
+-mapq $mapq
+-g @GENOME_FILE@
+-i '$input'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
-        <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
+        <param name="input" argument="-i" type="data" format="bed" label="Convert the following BED file to BAM"/>
+        <param argument="-bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
             label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format"
-            help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/>
+            help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string"/>
         <expand macro="input_conditional_genome_file" />
-        <param name="mapq" type="integer" value="255"
-            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/>
+        <param argument="-mapq" type="integer" value="255"
+            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
     </inputs>
     <outputs>
-        <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
+        <data name="output" format="bam" metadata_source="input" label="${input.name} (as BAM)"/>
     </outputs>
     <tests>
         <test>
@@ -35,14 +33,12 @@
             <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 bedToIgv.xml
--- a/bedToIgv.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bedToIgv.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,26 +1,24 @@
-<tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@TOOL_VERSION@">
     <description>create batch script for taking IGV screenshots</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedToIgv
-        -i '$input'
-        #if $sort:
-            -sort $sort
-        #end if
-        $clps
-        $name
-        -slop $slop
-        -img $img
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedToIgv
+-i '$input'
+#if $sort:
+    -sort $sort
+#end if
+$clps
+$name
+-slop $slop
+-img $img
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Create IGV batch script for this @STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Create IGV batch script for this @STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="sort" type="select" label="Sort BAM file by" help="The type of BAM sorting you would like to apply to each image.">
             <option value="">No sorting at all (default)</option>
             <option value="base">base</option>
@@ -30,17 +28,17 @@
             <option value="sample">sample</option>
             <option value="readGroup">readGroup</option>
         </param>
-        <param name="clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/>
-        <param name="name" type="boolean" truevalue="-name" falsevalue="" label="Use the name field (column 4) for each image's filename." help="Default is to use chr:start-pos."/>
-        <param name="slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/>
-        <param name="img" type="select" label="Select the type of image to be created.">
-            <option value="png">png</option>
-            <option value="eps">eps</option>
-            <option value="svg">svg</option>
+        <param argument="-clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/>
+        <param argument="-name" type="boolean" truevalue="-name" falsevalue="" label="Use the name field (column 4) for each image's filename." help="Default is to use chr:start-pos."/>
+        <param argument="-slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/>
+        <param argument="-img" type="select" label="Select the type of image to be created.">
+            <option value="png">PNG</option>
+            <option value="eps">EPS</option>
+            <option value="svg">SVG</option>
         </param>
     </inputs>
     <outputs>
-        <data format="txt" name="output" metadata_source="input" label="BED to IGV on ${input.name}"/>
+        <data name="output" format="txt" metadata_source="input" label="BED to IGV on ${input.name}"/>
     </outputs>
     <tests>
         <test>
@@ -48,8 +46,7 @@
             <output name="output" file="igv_bed_script.txt" ftype="txt" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Creates a batch script to create IGV images at each interval defined in a @STD_BEDTOOLS_INPUT_LABEL@ file.
@@ -60,7 +57,6 @@
 (2)  It is assumed that prior to running the script, you've loaded the proper genome and tracks.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 bedpeToBam.xml
--- a/bedpeToBam.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bedpeToBam.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,28 +1,25 @@
-<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools bedpetobam
-            -mapq $mapq
-            -i '$input'
-            -g @GENOME_FILE@
-            > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools bedpetobam
+-mapq $mapq
+-i '$input'
+-g @GENOME_FILE@
+> '$output'
+    ]]></command>
     <inputs>
-        <param name="input" format="bed,gff,vcf" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
-        <param name="mapq" type="integer" value="255"
-            label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
-            help="(-mapq)" />
+        <param argument="-mapq" type="integer" value="255"
+            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
     </inputs>
     <outputs>
-        <data format="bam" name="output" metadata_source="input"/>
+        <data name="output" format="bam" metadata_source="input"/>
     </outputs>
     <tests>
         <test>
@@ -32,8 +29,7 @@
             <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Converts feature records to BAM format.
@@ -43,7 +39,6 @@
 BED files must be at least BED4 to create BAM (needs name field).
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 closestBed.xml
--- a/closestBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/closestBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@">
     <description>find the closest, potentially non-overlapping interval</description>
     <macros>
         <import>macros.xml</import>
@@ -24,13 +24,15 @@
 #if str($overlap_with.source) == "data_table":
     -b '$overlap_with.table.fields.path'
 #else
-    #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.inputB])
-    -b '$inputBs'
+    -b
+    #for $file in $overlap_with.inputB:
+        '$file'
+    #end for
 #end if
 > '$output'
     ]]></command>
     <inputs>
-        <param name="inputA" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <!-- overlap with file (inputB) -->
         <conditional name="overlap_with">
             <param name="source" type="select" label="Overlap with: will you select a @STD_BEDTOOLS_INPUT_LABEL@ file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
@@ -46,7 +48,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="inputB" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" />
+                <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" />
             </when>
         </conditional>
 
@@ -100,7 +102,7 @@
     </inputs>
     <outputs>
         <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} -->
-        <!-- <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> -->
+        <!-- <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> -->
         <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" />
     </outputs>
     <tests>
diff -r 87ee588b3d45 -r dde39ba9c031 clusterBed.xml
--- a/clusterBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/clusterBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,29 +1,27 @@
-<tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@TOOL_VERSION@">
     <description>cluster overlapping/nearby intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools cluster
-        $strand
-        -d $distance
-        -i '$inputA'
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools cluster
+$strand
+-d $distance
+-i '$inputA'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness."
+        <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness."
             help="That is, only cluster features that are the same strand. By default, this is disabled." />
-        <param name="distance" type="integer" value="0"
+        <param name="distance" argument="-d" type="integer" value="0"
             label="Maximum distance between features allowed for features to be clustered"
             help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA"/>
+        <data name="output" format_source="inputA" metadata_source="inputA"/>
     </outputs>
     <tests>
         <test>
@@ -31,8 +29,7 @@
             <output name="output" file="clusterBed_result.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Similar to merge, cluster report each set of overlapping or “book-ended” features in an interval file. In contrast to merge, cluster does not flatten the cluster of intervals into a new meta-interval; instead, it assigns an unique cluster ID to each record in each cluster. This is useful for having fine control over how sets of overlapping intervals in a single interval file are combined.
@@ -44,7 +41,6 @@
 bedtools cluster requires that you presort your data by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files).
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 complementBed.xml
--- a/complementBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/complementBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,24 +1,22 @@
-<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@">
     <description>Extract intervals not represented by an interval file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        complementBed
-        -i "$input"
-        -g @GENOME_FILE@
-        > "$output"
-]]>
-    </command>
+    <command><![CDATA[
+complementBed
+-i '$input'
+-g @GENOME_FILE@
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
     </inputs>
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" label="Complement of ${input.name}"/>
+        <data name="output" format_source="input" metadata_source="input" label="Complement of ${input.name}"/>
     </outputs>
     <tests>
         <test>
@@ -28,8 +26,7 @@
             <output name="output" file="complementBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input @STD_BEDTOOLS_INPUT_LABEL@ file.
@@ -37,7 +34,6 @@
 .. image:: $PATH_TO_IMAGES/complement-glyph.png
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 coverageBed.xml
--- 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>
diff -r 87ee588b3d45 -r dde39ba9c031 expandBed.xml
--- a/expandBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/expandBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,24 +1,22 @@
-<tool id="bedtools_expandbed" name="bedtools ExpandBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_expandbed" name="bedtools ExpandBed" version="@TOOL_VERSION@">
     <description>replicate lines based on lists of values in columns</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools expand
-        -c "${cols}"
-        -i "${input}"
-        > "${output}"
-]]>
-    </command>
+    <command><![CDATA[
+bedtools expand
+-c '${cols}'
+-i '${input}'
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="choose_columns" />
     </inputs>
     <outputs>
-        <data name="output" metadata_source="input" format_source="input" />
+        <data name="output" format_source="input" metadata_source="input" />
     </outputs>
     <tests>
         <test>
@@ -32,14 +30,12 @@
             <output name="output" file="expandBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Replicate lines in a file based on columns of comma-separated values.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 fisherBed.xml
--- a/fisherBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/fisherBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,37 +1,35 @@
-<tool id="bedtools_fisher" name="bedtools FisherBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@+galaxy1">
     <description>calculate Fisher statistic between two feature files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools fisher
-        $strand
-        $split
-        -a '$inputA'
-        -b '$inputB'
-        -f $overlap
-        -g @GENOME_FILE@
-        $reciprocal
-        $m
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools fisher
+$strand
+$split
+-a '$inputA'
+-b '$inputB'
+@OVERLAP@
+-g @GENOME_FILE@
+$reciprocal
+$m
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
         <expand macro="strand2" />
         <expand macro="split" />
         <expand macro="overlap" />
         <expand macro="reciprocal" />
-        <param name="m" type="boolean" checked="False" truevalue="-m" falsevalue=""
-            label="Merge overlapping intervals before looking at overlap" help="(-m)" />
+        <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false"
+            label="Merge overlapping intervals before looking at overlap" />
     </inputs>
     <outputs>
-        <data name="output" metadata_source="inputA" format_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
+        <data name="output" format_source="inputA" metadata_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
     </outputs>
     <tests>
         <test>
@@ -42,14 +40,12 @@
             <output name="output" file="fisherBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 flankBed.xml
--- a/flankBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/flankBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,40 +1,38 @@
-<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@">
     <description>create new intervals from the flanks of existing intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        flankBed
-        $pct
-        $strand
-        -g @GENOME_FILE@
-        -i '$input'
+    <command><![CDATA[
+flankBed
+$pct
+$strand
+-g @GENOME_FILE@
+-i '$input'
 
-        #if $addition.addition_select == 'b':
-            -b $addition.b
-        #else:
-            -l $addition.l
-            -r $addition.r
-        #end if
-        > '$output'
-]]>
-    </command>
+#if $addition.addition_select == 'b':
+    -b $addition.b
+#else:
+    -l $addition.l
+    -r $addition.r
+#end if
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
-        <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
+        <param argument="-pct" type="boolean" truevalue="-pct" falsevalue="" checked="false"
             label="Define -l and -r as a fraction of the feature’s length"
-            help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. (-pct)" />
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
+            help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
             label="Define -l and -r based on strand"
-            help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate. (-s)" />
+            help="For example, if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
         <expand macro="addition" />
     </inputs>
     <outputs>
-        <data metadata_source="input" format_source="input" name="output" />
+        <data name="output" format_source="input" metadata_source="input" />
     </outputs>
     <tests>
         <test>
@@ -55,8 +53,7 @@
             <output name="output" file="flankBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.
@@ -67,12 +64,9 @@
 
 In order to prevent creating intervals that violate chromosome boundaries, bedTools flank requires a bedTool genome file defining the length of each chromosome or contig. . This should be a two column tabular file with the chromosome name in the first column and the END coordinate of the chromosome in the second column.
 
-If you need this data for any genome that is at UCSC (http://genome.ucsc.edu), it can be extracted from the Table Browser with the "Get Data: UCSC Main" tool. Set "group" to "All Tables", "table" to "chromInfo", and "output format" to "all fields from selected table". 
-
-
+If you need this data for any genome that is at UCSC (http://genome.ucsc.edu), it can be extracted from the Table Browser with the "Get Data: UCSC Main" tool. Set "group" to "All Tables", "table" to "chromInfo", and "output format" to "all fields from selected table".
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 genomeCoverageBed.xml
--- a/genomeCoverageBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/genomeCoverageBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,41 +1,38 @@
-<tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@WRAPPER_VERSION@">
+<tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@TOOL_VERSION@">
     <description>compute the coverage over an entire genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools genomecov
-        @GENOME_FILE_COVERAGE@
+    <command><![CDATA[
+bedtools genomecov
+@GENOME_FILE_COVERAGE@
+
+$split
+$strand
 
-        $split
-        $strand
-
-        #if str($report.report_select) == "bg":
-            #if $report.zero_regions:
-                $report.zero_regions
-            #else:
-                -bg
-            #end if
+#if str($report.report_select) == "bg":
+    #if $report.zero_regions:
+        $report.zero_regions
+    #else:
+        -bg
+    #end if
 
-            #if str($report.scale):
-              -scale $report.scale
-            #end if
-        #else:
-            #if str($report.max):
-              -max $report.max
-            #end if
-        #end if
-        $d
-        $dz
-        $five
-        $three
-
-        > '$output'
-]]>
-    </command>
+    #if str($report.scale):
+        -scale $report.scale
+    #end if
+#else:
+    #if str($report.max):
+        -max $report.max
+    #end if
+#end if
+$d
+$dz
+$five
+$three
+> '$output'
+    ]]></command>
     <inputs>
         <conditional name="input_type">
             <param name="input_type_select" type="select" label="Input type">
@@ -43,11 +40,11 @@
                 <option value="bam">BAM</option>
             </param>
             <when value="bed">
-                <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
+                <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
                 <expand macro="input_conditional_genome_file" />
             </when>
             <when value="bam">
-                <param format="bam" name="input" type="data" label="BAM file" />
+                <param name="input" argument="-ibam" type="data" format="bam" label="BAM file" />
             </when>
         </conditional>
         <conditional name="report">
@@ -56,35 +53,35 @@
                 <option value="hist">Data suiteable for Histogram</option>
             </param>
             <when value="bg">
-                <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue=""
-                    label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported.  (-bga)" />
-                <param name="scale" type="float" value="1.0"
+                <param name="zero_regions" argument="-bga" type="boolean" truevalue="-bga" falsevalue="" checked="false"
+                    label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported" />
+                <param argument="-scale" type="float" value="1.0"
                     label="Scale the coverage by a constant factor"
-                    help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)" />
+                    help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM)." />
             </when>
             <when value="hist">
-                <param name="max" type="integer" label="Specify max depth" value="0"
-                    help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)" />
+                <param argument="-max" type="integer" value="0" label="Specify max depth"
+                    help="Combine all positions with a depth >= max into a single bin in the histogram" />
             </when>
         </conditional>
         <expand macro="split" />
-        <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)">
+        <param argument="-strand" type="select" label="Calculate coverage based on">
             <option value="">both strands combined</option>
             <option value="-strand +">positive strand only</option>
             <option value="-strand -">negative strand only</option>
         </param>
 
-        <param name="d" type="boolean" checked="False" truevalue="-d" falsevalue=""
-            label="Report the depth at each genome position with 1-based coordinates" help="(-d)" />
-        <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue=""
-            label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" />
-        <param name="five" type="boolean" checked="False" truevalue="-5" falsevalue=""
-            label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" />
-        <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue=""
-            label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" />
+        <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
+            label="Report the depth at each genome position with 1-based coordinates" />
+        <param argument="-dz" type="boolean" truevalue="-dz" falsevalue="" checked="false"
+            label="Report the depth at each genome position with 0-based coordinatess" />
+        <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" checked="false"
+            label="Calculate coverage of 5’ positions" help="Instead of entire interval" />
+        <param name="three" argument="-3" type="boolean" truevalue="-3" falsevalue="" checked="false"
+            label="Calculate coverage of 3’ positions" help="Instead of entire interval" />
     </inputs>
     <outputs>
-        <data format="bedgraph" name="output">
+        <data name="output" format="bedgraph">
             <change_format>
                 <when input="report.report_select" value="hist" format="tabular" />
             </change_format>
@@ -100,8 +97,7 @@
             <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format.
@@ -168,7 +164,6 @@
 
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 getfastaBed.xml
--- a/getfastaBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/getfastaBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,36 +1,34 @@
-<tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@">
     <description>use intervals to extract sequences from a FASTA file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        #if str( $fasta_source.fasta_source_selector ) == 'history':
-          #set $fasta_file = $fasta_source.fasta
-        #else
-          #set $fasta_file = $fasta_source.fasta_id.fields.path
-        #end if
-        bedtools getfasta
-        $name
-        $tab
-        $strand
-        $split
-        -fi '$fasta_file'
-        -bed '$input'
-        -fo '$output'
-]]>
-    </command>
+    <command><![CDATA[
+#if str($fasta_source.fasta_source_selector) == 'history':
+    #set $fasta_file = $fasta_source.fasta
+#else
+    #set $fasta_file = $fasta_source.fasta_id.fields.path
+#end if
+bedtools getfasta
+$name
+$tab
+$strand
+$split
+-fi '$fasta_file'
+-bed '$input'
+-fo '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
+        <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
         <conditional name="fasta_source">
-            <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file">
-                <option value="history" selected="True">History</option>
+            <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
+                <option value="history" selected="true">History</option>
                 <option value="preloaded">Server indexed files</option>
             </param>
             <when value="history">
-                <param name="fasta" format="fasta" type="data" label="Fasta file" />
+                <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file" />
             </when>
             <when value="preloaded">
                <param name="fasta_id" type="select">
@@ -38,19 +36,17 @@
                </param>
             </when>
         </conditional>
-        <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
-            label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file"
-            help="(-name)" />
-        <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue=""
-            label="Report extract sequences in a tab-delimited format instead of in FASTA format"
-            help="(-tab)" />
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
+        <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false"
+            label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" />
+        <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false"
+            label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
             label="Force strandedness"
-            help="If the feature occupies the antisense strand, the sequence will be reverse complemented. (-s)" />
+            help="If the feature occupies the antisense strand, the sequence will be reverse complemented" />
         <expand macro="split" />
     </inputs>
     <outputs>
-        <data format="fasta" name="output">
+        <data name="output" format="fasta">
             <change_format>
                 <when input="tab" value="-tab" format="tabular" />
             </change_format>
@@ -72,8 +68,7 @@
             <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools getfasta will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: “>chrom>:&lt;start>-&lt;end>”.
@@ -87,7 +82,6 @@
 2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold -w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 groupbyBed.xml
--- a/groupbyBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/groupbyBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,32 +1,30 @@
-<tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@">
     <description>group by common cols and summarize other cols</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools groupby
-        -i "${inputA}"
-        -g '$group'
-        -c "${cols}"
-        -o $operation
-        > "${output}"
-]]>
-    </command>
+    <command><![CDATA[
+bedtools groupby
+-i '${inputA}'
+-g '$group'
+-c '${cols}'
+-o $operation
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="choose_columns" />
-        <param name="group" type="text" value="1,2,3"
+        <param name="group" argument="-g" type="text" value="1,2,3"
             label="Specifies which column(s) (1-based) should be used to group the input"
-            help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. (-g)">
+            help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed.">
             <sanitizer invalid_char="">
                 <valid initial="string.digits"><add value=","/><add value="-"/></valid>
             </sanitizer>
         </param>
-        <param name="operation" type="select" label="Specify the operation" help="(-o)">
-            <option value="sum" selected="True">Sum - numeric only</option>
+        <param name="operation" argument="-o" type="select" label="Specify the operation">
+            <option value="sum" selected="true">Sum - numeric only</option>
             <option value="stdev">Stdev - numeric only</option>
             <option value="sstdev">Sstdev - numeric only</option>
             <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option>
@@ -38,7 +36,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA"/>
+        <data name="output" format_source="inputA" metadata_source="inputA"/>
     </outputs>
     <tests>
         <test>
@@ -63,14 +61,12 @@
             <output name="output" file="groupbyBed_result3.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Replicate lines in a file based on columns of comma-separated values.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 intersectBed.xml
--- a/intersectBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/intersectBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@WRAPPER_VERSION@">
+<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1">
     <description>find overlapping intervals in various ways</description>
     <macros>
         <import>macros.xml</import>
@@ -8,76 +8,82 @@
     </expand>
     <expand macro="stdio" />
     <command><![CDATA[
-        #import re
-        #set modes = ' '.join( str($overlap_mode).split(',') )
+#import re
+#set modes = ' '.join(str($overlap_mode).split(','))
+
+#if $modes == "None":
+    #set modes = ''
+#end if
 
-        #if $modes == "None":
-            #set modes = ''
-        #end if
+bedtools intersect
+#if $inputA.is_of_type('bam'):
+    -abam '${inputA}'
+#else:
+    -a '${inputA}'
+#end if
 
-        bedtools intersect
-        #if $inputA.is_of_type('bam'):
-            -abam '${inputA}'
-        #else:
-            -a '${inputA}'
-        #end if
+#if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
+    -b '$reduce_or_iterate.inputB'
+#else:
+    -b
+    #for $file in $reduce_or_iterate.inputB
+        '$file'
+    #end for
 
-        #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'
-            #if $reduce_or_iterate.names:
-                #set namesB = "' '".join([re.sub('[^\s\w\-]', '_', str($file.element_identifier)) for $file in $reduce_or_iterate.inputB])
-                -names '$namesB'
-            #end if
+    #if $reduce_or_iterate.names:
+        #set namesB = "' '".join([re.sub('[^\s\w\-]', '_', str($file.element_identifier)) for $file in $reduce_or_iterate.inputB])
+        -names '$namesB'
+    #end if
+#end if
+$split
+$strand
+#if $fraction_cond.fraction_select == "specify":
+    #if str($fraction_cond.overlap)
+        -f $fraction_cond.overlap
+    #end if
+    $fraction_cond.reciprocal_cond.reciprocal
+    #if str($fraction_cond.reciprocal_cond.reciprocal) == '':
+        #if str($fraction_cond.reciprocal_cond.overlapB):
+            -F $fraction_cond.reciprocal_cond.overlapB
         #end if
-        $split
-        $strand
-        #if $fraction_cond.fraction_select == "specify":
-            -f '${fraction_cond.overlap}'
-            $fraction_cond.reciprocal_cond.reciprocal 
-            #if str($fraction_cond.reciprocal_cond.reciprocal) == '':
-                -F '${fraction_cond.reciprocal_cond.overlapB}'
-                $fraction_cond.reciprocal_cond.disjoint
-            #end if
-        #end if
-        $invert
-        $once
-        $header
-        $modes
-        $sorted
-        #if str($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
-        $bed
-        $count
-        > '${output}'
-]]>
-    </command>
+        $fraction_cond.reciprocal_cond.disjoint
+    #end if
+#end if
+$invert
+$once
+$header
+$modes
+$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 $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
+    #end if
+#end if
+$bed
+$count
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A to intersect with B" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
+        <param name="inputA" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A to intersect with B" 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 intersections of any 'input B' lines with A </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 intersections of any 'input B' lines with A</option>
             </param>
-            <when value='iterate'>
-                <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data"
-                       label="File(s) B to intersect with A" 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 to intersect with A" 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 to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
-                <param argument="names" type="boolean" truevalue="yes" falsevalue="no" label="add data set names instead of indices" help=""/>
+                <param argument="-names" type="boolean" truevalue="yes" falsevalue="no" label="Add data set names instead of indices" />
             </when>
         </conditional>
         <expand macro="strand2" />
-        <param name="overlap_mode" type="select" multiple="True" label="What should be written to the output file?">
+        <param name="overlap_mode" type="select" multiple="true" label="What should be written to the output file?">
             <option value="-wa">Write the original entry in A for each overlap (-wa)</option>
             <option value="-wb">Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by the fraction- and reciprocal option (-wb)</option>
             <option value="-wo">Write the original A and B entries plus the number of base pairs of overlap between the two features. Only A features with overlap are reported. Restricted by the fraction- and reciprocal option (-wo)</option>
@@ -87,46 +93,45 @@
 
         <expand macro="split" />
         <conditional name="fraction_cond">
-            <param name='fraction_select' type='select' label='Required overlap'>
-                <option value='default' selected='true'>Default: 1bp</option>
-                <option value='specify'>Specify minimum overlap(s)</option>
+            <param name="fraction_select" type="select" label="Required overlap">
+                <option value="default" selected="true">Default: 1bp</option>
+                <option value="specify">Specify minimum overlap(s)</option>
             </param>
             <when value="default"/>
-            <when value='specify'>
+            <when value="specify">
                 <expand macro="overlap" />
                 <conditional name="reciprocal_cond">
                     <expand macro="reciprocal" />
                 <when value="-r"/>
                 <when value="">
-                    <expand macro="overlapB" />
-                    <param name="disjoint" argument="-e" type="boolean" checked="false" truevalue="-e"  falsevalue=""
+                    <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
+                    <param name="disjoint" argument="-e" type="boolean" truevalue="-e"  falsevalue="" checked="false"
                         label="Require that the fraction of overlap is fulfilled for A OR B." help="If enabled, then for -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered, otherwise, both fractions would have to be satisfied."/>
                 </when>
             </conditional>
             </when>
         </conditional>
         <!-- -v -->
-        <param name="invert" type="boolean" checked="false" truevalue="-v" falsevalue=""
-            label="Report only those alignments that **do not** overlap with file(s) B"
-            help="(-v)"/>
+        <param name="invert" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="false"
+            label="Report only those alignments that **do not** overlap with file(s) B" />
         <!-- -u -->
-        <param name="once" type="boolean" checked="false" truevalue="-u" falsevalue=""
+        <param name="once" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false"
             label="Write the original A entry _once_ if _any_ overlaps found in B."
-            help="Just report the fact >=1 hit was found. (-u)" />
+            help="Just report the fact >=1 hit was found" />
         <!-- -c -->
-        <param name="count" type="boolean" checked="false" truevalue="-c" falsevalue=""
+        <param name="count" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
             label="For each entry in A, report the number of overlaps with B."
-            help="Reports 0 for A entries that have no overlap with B. (-c)" />
+            help="Reports 0 for A entries that have no overlap with B" />
         <!-- -bed -->
-        <param argument="-bed" type="boolean" checked="false" truevalue="-bed" falsevalue=""
+        <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
             label="When using BAM input (-abam), write output as BED instead of BAM." />
         <!-- -sorted -g  -->
-        <param argument="-sorted" type="boolean" checked="false" truevalue="-sorted" falsevalue=""
+        <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
             label="For coordinate sorted input file the more efficient sweeping algorithm is enabled." />
         <expand macro="print_header" />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA">
+        <data name="output" format_source="inputA" metadata_source="inputA">
             <change_format>
                 <when input="bed" value="-bed" format="bed" />
             </change_format>
@@ -137,7 +142,7 @@
         <test>
             <param name="inputA" value="intersect-A.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
             <output name="output" file="intersect-default.bed" ftype="bed" />
@@ -145,7 +150,7 @@
         <test>
             <param name="inputA" value="intersect-query.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="reduce" />
+                <param name="reduce_or_iterate_selector" value="reduce" />
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             </conditional>
             <output name="output" file="intersect-multiple.bed" ftype="bed" />
@@ -153,7 +158,7 @@
         <test>
             <param name="inputA" value="intersect-query.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="reduce" />
+                <param name="reduce_or_iterate_selector" value="reduce" />
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
@@ -161,10 +166,10 @@
             <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
         </test>
         <test>
-                <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
+            <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             <param name="inputA" value="intersect-query.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="reduce" />
+                <param name="reduce_or_iterate_selector" value="reduce" />
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
                 <param name="names" value="yes" />
             </conditional>
@@ -175,7 +180,7 @@
         <test>
             <param name="inputA" value="intersect-query.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="reduce" />
+                <param name="reduce_or_iterate_selector" value="reduce" />
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             </conditional>
             <param name="invert" value="-v" />
@@ -185,12 +190,12 @@
         <test>
             <param name="inputA" value="intersect-query.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="reduce" />
+                <param name="reduce_or_iterate_selector" value="reduce" />
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
             <conditional name="fraction_cond">
-                <param name='fraction_select' value='specify'/>
+                <param name="fraction_select" value="specify"/>
                 <param name="overlap" value="1.0" />
             </conditional>
             <param name="sorted" value="-sorted" />
@@ -199,7 +204,7 @@
         <test>
             <param name="inputA" value="intersect-A.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wa" />
@@ -208,7 +213,7 @@
         <test>
             <param name="inputA" value="intersect-A.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wb" />
@@ -217,7 +222,7 @@
         <test>
             <param name="inputA" value="intersect-A.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
@@ -226,7 +231,7 @@
         <test>
             <param name="inputA" value="intersect-A.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-loj" />
@@ -235,7 +240,7 @@
         <test>
             <param name="inputA" value="intersect-A.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wo" />
@@ -244,7 +249,7 @@
         <test>
             <param name="inputA" value="intersect-A.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wao" />
@@ -253,7 +258,7 @@
         <test>
             <param name="inputA" value="intersect-A.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
             <param name="once" value="-u" />
@@ -262,7 +267,7 @@
         <test>
             <param name="inputA" value="intersect-A.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
             <param name="count" value="-c"/>
@@ -271,7 +276,7 @@
         <test>
             <param name="inputA" value="intersect-A.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
             <param name="invert" value="-v"/>
@@ -280,12 +285,12 @@
         <test>
             <param name="inputA" value="intersect-A2.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
             <conditional name="fraction_cond">
-                <param name='fraction_select' value='specify'/>
+                <param name="fraction_select" value="specify"/>
                 <param name="overlap" value="0.5" />
             </conditional>
             <output name="output" file="intersect-fracA.bed" ftype="bed" />
@@ -293,12 +298,12 @@
         <test>
             <param name="inputA" value="intersect-A2.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
             <conditional name="fraction_cond">
-                <param name='fraction_select' value='specify'/>
+                <param name="fraction_select" value="specify"/>
                 <param name="overlap" value="0.5" />
                 <conditional name="reciprocal_cond">
                     <param name="reciprocal" value="-r" />
@@ -309,12 +314,12 @@
         <test>
             <param name="inputA" value="intersect-A2.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
             <conditional name="fraction_cond">
-                <param name='fraction_select' value='specify'/>
+                <param name="fraction_select" value="specify"/>
                 <param name="overlap" value="0.5" />
                 <conditional name="reciprocal_cond">
                     <param name="overlapB" value="0.5" />
@@ -325,12 +330,12 @@
         <test>
             <param name="inputA" value="intersect-A2.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
-                <param name='reduce_or_iterate_selector' value="iterate" />
+                <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
             <conditional name="fraction_cond">
-                <param name='fraction_select' value='specify'/>
+                <param name="fraction_select" value="specify"/>
                 <param name="overlap" value="0.5" />
                 <conditional name="reciprocal_cond">
                     <param name="overlapB" value="0.5" />
@@ -362,8 +367,7 @@
             <output name="output" file="intersectBed_result3.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with both @STD_BEDTOOLS_INPUT_LABEL@ and BAM files as input.
@@ -379,7 +383,6 @@
 Note that a BAM alignment will be sent to the output file **once** even if it overlaps more than one interval in the BED file.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 jaccardBed.xml
--- a/jaccardBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/jaccardBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,35 +1,37 @@
-<tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@+galaxy1">
     <description>calculate the distribution of relative distances between two files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools jaccard
-            $strand
-            $split
-            $reciprocal
-            -f $overlap
-            -a '$inputA'
-            -b '$inputB'
-            > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools jaccard
+$strand
+$split
+$reciprocal
+@OVERLAP@
+#if str($overlapB):
+   -F $overlapB
+#end if
+-a '$inputA'
+-b '$inputB'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="overlap" />
+        <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
         <expand macro="reciprocal" />
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
             label="Force strandedness"
-            help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand. (-s)" />
+            help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand." />
         <expand macro="strand2" />
         <expand macro="split" />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
+        <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
     </outputs>
     <tests>
         <test>
@@ -44,8 +46,7 @@
             <output name="output" file="jaccardBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-
+    <help><![CDATA[
 **What it does**
 
 By default, bedtools jaccard reports the length of the intersection, the length of the union (minus the intersection), the final Jaccard statistic reflecting the similarity of the two sets, as well as the number of intersections.
@@ -58,6 +59,6 @@
 The jaccard tool requires that your data is pre-sorted by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files).
 
 @REFERENCES@
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 linksBed.xml
--- a/linksBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/linksBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,26 +1,24 @@
-<tool id="bedtools_links" name="bedtools LinksBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_links" name="bedtools LinksBed" version="@TOOL_VERSION@">
     <description>create a HTML page of links to UCSC locations</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools links
-            -base "${basename}"
-            -org "${org}"
-            -db "${db}"
-            -i "${input}"
-            > "${output}"
-]]>
-    </command>
+    <command><![CDATA[
+bedtools links
+-base '${basename}'
+-org '${org}'
+-db '${db}'
+-i '${input}'
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param name="basename" type="text" value="http://genome.ucsc.edu"
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="basename" argument="-base" type="text" value="http://genome.ucsc.edu"
             label="The 'basename' for the UCSC genome browser" />
-        <param name="org" type="text" value="human" label="Organism name" help="e.g. mouse, human (-org)" />
-        <param name="db" type="text" value="hg19" label="The genome build" help="(-db)"/>
+        <param argument="-org" type="text" value="human" label="Organism name" help="E.g. mouse, human" />
+        <param argument="-db" type="text" value="hg19" label="The genome build" />
     </inputs>
     <outputs>
         <data name="output" format="html" />
@@ -41,14 +39,12 @@
             <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 macros.xml
--- a/macros.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/macros.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,14 +1,14 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@WRAPPER_VERSION@">bedtools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">bedtools</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">2.27.1</token>
+    <token name="@TOOL_VERSION@">2.27.1</token>
     <token name="@SAMTOOLS_VERSION@">1.9</token>
     <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf</token>
-    <token name="@STD_BEDTOOLS_INPUT_LABEL@">bed,bedgraph,gff,vcf</token>
+    <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
@@ -22,44 +22,49 @@
     </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="" selected="true">No</option>
             <option value="-r">Yes</option>
         </param>
     </xml>
-    <xml name="overlap">
-        <param name="overlap" argument="-f" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp."/>
+    <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>
-    <xml name="overlapB">
-        <param name="overlapB" argument="-F" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" 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="" 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?" help="(-seed)">
-                <option value="False" selected="True">Random Shuffling</option>
+            <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 name="seed" type="integer" value="12345" label="Enter Seed" />
+                <param argument="-seed" type="integer" value="12345" label="Enter Seed" />
             </when>
             <when value="False" />
         </conditional>
     </xml>
     <xml name="split">
-        <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue=""
+        <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. (-split)" />
+            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="loc" selected="true">Locally installed Genome file</option>
                 <option value="hist">Genome file from your history</option>
             </param>
             <when value="loc">
@@ -107,38 +112,38 @@
 #end if
     </token>
     <token name="@GENOME_FILE_COVERAGE@">
-#if $input_type.input_type_select == "bed":
+#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
-#elif $input_type.input_type_select == "bam":
-    -ibam '$input_type.input'
 #end if
     </token>
     <xml name="closest_D_option">
-        <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue=""
+        <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'. (-iu)" />
+            help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
 
-        <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue=""
+        <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'. (-id)" />
+            help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
 
-        <param name="fu" type="boolean" checked="false" truevalue="-fu" falsevalue=""
+        <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'. (-fu)" />
+            help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
 
-        <param name="fd" type="boolean" checked="false" truevalue="-fd" falsevalue=""
+        <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'. (-fd)" />
+            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="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">
@@ -151,8 +156,8 @@
         </conditional>
     </xml>
     <xml name="print_header">
-        <param name="header" type="boolean" checked="False" truevalue="-header" falsevalue=""
-            label="Print the header from the A file prior to results" help="(-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">
@@ -162,9 +167,9 @@
 
     <!-- ToDo column_picker -->
     <xml name="choose_columns">
-        <param name="cols" type="text" value=""
+        <param name="cols" argument="-c" type="text" value=""
             label="Specify the column(s) that should be summarized"
-            help="comma separated (-c)">
+            help="Comma separated">
             <sanitizer invalid_char="">
                 <valid initial="string.digits"><add value=","/></valid>
             </sanitizer>
@@ -201,7 +206,7 @@
     </xml>
 
     <xml name="math_options">
-        <option value="sum" selected="True">Sum - numeric only</option>
+        <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>
diff -r 87ee588b3d45 -r dde39ba9c031 makeWindowsBed.xml
--- a/makeWindowsBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/makeWindowsBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,39 +1,37 @@
-<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@">
     <description>make interval windows across a genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools makewindows
-        #if $type.type_select == 'genome':
-            @GENOME_FILE_MAKEWINDOWS@
-        #else:
-            -b '$type.input'
-        #end if
-        #if $action.action_select == 'windowsize':
-            -w $action.windowsize
-            #if $action.step_size.step_size_select == 'yes':
-                -s $action.step_size.step_size
-            #end if
-        #else:
-            -n $action.number
-            -s $action.step_size
-        #end if
-        $sourcename
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools makewindows
+#if $type.type_select == 'genome':
+    @GENOME_FILE_MAKEWINDOWS@
+#else:
+    -b '$type.input'
+#end if
+#if $action.action_select == 'windowsize':
+    -w $action.windowsize
+    #if $action.step_size.step_size_select == 'yes':
+        -s $action.step_size.step_size
+    #end if
+#else:
+    -n $action.number
+    -s $action.step_size
+#end if
+$sourcename
+> '$output'
+    ]]></command>
     <inputs>
          <conditional name="type">
             <param name="type_select" type="select" label="Work with">
-                <option value="bed" selected="True">Bed File</option>
+                <option value="bed" selected="true">Bed File</option>
                 <option value="genome">Genome File</option>
             </param>
             <when value="bed">
-                <param  name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+                <param name="input" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
             </when>
             <when value="genome">
                 <expand macro="input_conditional_genome_file" />
@@ -41,11 +39,11 @@
         </conditional>
         <conditional name="action">
             <param name="action_select" type="select" label="Work with">
-                <option value="windowsize" selected="True">Set WindowSize</option>
+                <option value="windowsize" selected="true">Set WindowSize</option>
                 <option value="number">Give Number of Windows</option>
             </param>
             <when value="windowsize">
-                <param name="windowsize" type="integer" value="1"
+                <param name="windowsize" argument="-w" type="integer" value="1"
                     label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows"
                     help="i.e. same number of nucleotide in each window" />
                  <conditional name="step_size">
@@ -53,23 +51,23 @@
                         label="Specify Step size? i.e. how many base pairs to step before creating a new window"
                         help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
                         <option value="yes">Yes</option>
-                        <option value="no" selected="True">No</option>
+                        <option value="no" selected="true">No</option>
                     </param>
                     <when value="yes">
-                        <param name="step_size" type="integer" value="100" label="Specify it" />
+                        <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
                     </when>
                     <when value="no" />
                  </conditional>
             </when>
             <when value="number">
-                <param name="number" type="integer" value="1"
+                <param name="number" argument="-n" type="integer" value="1"
                     label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows"
-                    help="i.e. same number of windows, with varying window sizes" />
-                <param name="step_size" type="integer" value="100" label="Specify it" />
+                    help="I.e. same number of windows, with varying window sizes" />
+                <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
             </when>
         </conditional>
         <param name="sourcename" type="select" label="ID Naming Options">
-            <option value="" selected="True">Default</option>
+            <option value="" selected="true">Default</option>
             <option value="-i src">use the source interval's name</option>
             <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option>
             <option value="-i srcwinnum">use the source interval's name with the window number.</option>
@@ -115,14 +113,12 @@
             <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Makes adjacent or sliding windows across a genome or BED file.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 mapBed.xml
--- a/mapBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/mapBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,32 +1,34 @@
-<tool id="bedtools_map" name="bedtools MapBed" version="@WRAPPER_VERSION@.2">
+<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2">
     <description>apply a function to a column for each overlapping interval</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
+    <command><![CDATA[
 bedtools map
 -a '${inputA}'
 -b '${inputB}'
 $strand
 @C_AND_O_ARGUMENT@
--f $overlap
+@OVERLAP@
+#if str($overlapB):
+    -F $overlapB
+#end if
 $reciprocal
 $split
 $header
 @GENOME_FILE_MAPBED@
 > '${output}'
-]]>
-    </command>
+    ]]></command>
     <inputs>
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
+        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
+        <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
         <expand macro="overlap" />
-        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
+        <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
+        <param name="reciprocal" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
             label="Require reciprocal overlap"
-            help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
+            help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval" />
         <expand macro="strand2" />
         <expand macro="c_and_o_argument">
             <param name="col" argument="-c" type="data_column" data_ref="inputB" label="Specify the column(s) from the B file to map onto intervals in A" help="Multiple columns can be specified in a comma-delimited list" />
@@ -34,7 +36,7 @@
         <expand macro="split" />
         <expand macro="print_header" />
         <conditional name="genome">
-            <param name="genome_choose" argument="-g" type="select" 
+            <param name="genome_choose" argument="-g" type="select"
                 label="Specify a genome file the defines the expected chromosome order in the input files." >
                 <option value="" selected="true">No</option>
                 <option value="-g">Yes</option>
@@ -46,7 +48,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
+        <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
     </outputs>
     <tests>
         <test>
@@ -101,8 +103,7 @@
             <output name="output" file="mapBed_result5.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools map allows one to map overlapping features in a B file onto features in an A file and apply statistics and/or summary operations on those features.
@@ -118,7 +119,6 @@
 The map tool is substantially faster in versions 2.19.0 and later. The plot below demonstrates the increased speed when, for example, counting the number of exome alignments that align to each exon. The bedtools times are compared to the bedops bedmap utility as a point of reference.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 maskFastaBed.xml
--- a/maskFastaBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/maskFastaBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,36 +1,34 @@
-<tool id="bedtools_maskfastabed" name="bedtools MaskFastaBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_maskfastabed" name="bedtools MaskFastaBed" version="@TOOL_VERSION@">
     <description>use intervals to mask sequences from a FASTA file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools maskfasta
-            $soft
-            -mc '${mc}'
-            -fi '${fasta}'
-            -bed '${input}'
-            -fo '${output}'
-            $fullheader
-]]>
-    </command>
+    <command><![CDATA[
+bedtools maskfasta
+$soft
+-mc '${mc}'
+-fi '${fasta}'
+-bed '${input}'
+-fo '${output}'
+$fullheader
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param format="fasta" name="fasta" type="data" label="Fasta file"/>
-        <param name="soft" type="boolean" checked="false" truevalue="-soft" falsevalue=""
+        <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file"/>
+        <param argument="-soft" type="boolean" truevalue="-soft" falsevalue="" checked="false"
             label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence"
-            help="By default, hard-masking (that is, conversion to Ns) is performed. (-soft)" />
-        <param name="mc" type="text"  value="N"
+            help="By default, hard-masking (that is, conversion to Ns) is performed" />
+        <param argument="-mc" type="text"  value="N"
             label="Replace masking character"
-            help="That is, instead of masking with Ns, use another character. (-mc)" />
+            help="That is, instead of masking with Ns, use another character" />
         <param argument="-fullHeader" name="fullheader" type="boolean" truevalue="-fullHeader" falsevalue=""
-            label="Use full fasta header." 
+            label="Use full fasta header."
             help="By default, only the word before the first space or tab is used"/>
     </inputs>
     <outputs>
-        <data format="fasta" name="output" />
+        <data name="output" format="fasta" />
     </outputs>
     <tests>
         <test>
@@ -53,8 +51,7 @@
             <output name="output" file="maskFastaBed_result3.fasta" ftype="fasta" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools maskfasta masks sequences in a FASTA file based on intervals defined in a feature file. The headers in the input FASTA file must exactly match the chromosome column in the feature file. This may be useful fro creating your own masked genome file based on custom annotations or for masking all but your target regions when aligning sequence data from a targeted capture experiment.
@@ -62,7 +59,6 @@
 .. image:: $PATH_TO_IMAGES/maskfasta-glyph.png
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 mergeBed.xml
--- a/mergeBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/mergeBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,39 +1,37 @@
-<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@WRAPPER_VERSION@">
+<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@">
     <description>combine overlapping/nearby intervals into a single interval</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        mergeBed
-            -i "${input}"
-            $strand
-            -d $distance
-            $header
-            @C_AND_O_ARGUMENT@
-            > "${output}"
-]]>
-    </command>
+    <command><![CDATA[
+mergeBed
+-i '${input}'
+$strand
+-d $distance
+$header
+@C_AND_O_ARGUMENT@
+> '${output}'
+    ]]></command>
     <inputs>
-        <param  name="input" format="bam,@STD_BEDTOOLS_INPUTS@" type="data" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param  name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="strand" type="select" label="Calculation based on strandedness?">
-            <option value="" selected="True">Overlaps on either strand</option>
-            <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
-            <option value="-S +">Force merge for forward strand only.</option>
-            <option value="-S -">Force merge for reverse strand only.</option>
+            <option value="" selected="true">Overlaps on either strand</option>
+            <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option>
+            <option value="-S +">Force merge for forward strand only (-S +)</option>
+            <option value="-S -">Force merge for reverse strand only (-S -)</option>
         </param>
-        <param name="distance" type="integer" value="0"
+        <param name="distance" argument="-d" type="integer" value="0"
             label="Maximum distance between features allowed for features to be merged"
-            help="That is, overlapping and/or book-ended features are merged. (-d)"/>
+            help="That is, overlapping and/or book-ended features are merged"/>
         <expand macro="print_header" />
         <expand macro="c_and_o_argument">
-            <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" />
+            <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" />
         </expand>
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
+        <data name="output" format="bed" metadata_source="input" label="Merged ${input.name}"/>
     </outputs>
     <tests>
         <test>
@@ -65,8 +63,7 @@
             <output name="output" file="mergedBed_result5.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.
@@ -143,7 +140,6 @@
 
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 multiCov.xml
--- a/multiCov.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/multiCov.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,75 +1,70 @@
-<tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@">
     <description>counts coverage from multiple BAMs at specific intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        #for $i, $bam in enumerate( $bams ):
-            ln -s -f $bam ${i}.bam &&
-            ln -s -f $bam.metadata.bam_index ${i}.bam.bai &&
-        #end for
+    <command><![CDATA[
+#for $i, $bam in enumerate($bams):
+    ln -s -f '$bam' ${i}.bam &&
+    ln -s -f '$bam.metadata.bam_index' ${i}.bam.bai &&
+#end for
 
-        bedtools multicov
-            -bed '$input'
-            -bams
-            #for $i, $bam in enumerate( $bams ):
-                '${i}.bam'
-            #end for
-            $strand
-            -f $overlap
-            $reciprocal
-            $split
-            -q $q
-            $duplicate
-            $failed
-            $proper
-            > '$output'
-]]>
-    </command>
+bedtools multicov
+-bed '$input'
+-bams
+#for $i, $bam in enumerate($bams):
+    '${i}.bam'
+#end for
+$strand
+@OVERLAP@
+$reciprocal
+$split
+-q $q
+$duplicate
+$failed
+$proper
+> '$output'
+    ]]></command>
     <inputs>
-        <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" />
+        <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" />
         <!-- Additional files, if the user needs more -->
-        <param name="bams" format="bam" type="data" multiple="True" label="BAM file" />
+        <param argument="-bams" type="data" format="bam" multiple="true" label="BAM file" />
 
         <expand macro="strand2" />
         <expand macro="overlap" />
         <expand macro="reciprocal" />
         <expand macro="split" />
-        <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" />
-        <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue=""
+        <param argument="-q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" />
+        <param name="duplicate" argument="-D" type="boolean" truevalue="-D" falsevalue="" checked="false"
             label="Include duplicate reads"
-            help="Default counts non-duplicates only. (-D)" />
-        <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue=""
+            help="Default counts non-duplicates only" />
+        <param name="failed" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="false"
             label="Include failed-QC reads"
-            help="Default counts pass-QC reads only (-F)"/>
-        <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue=""
+            help="Default counts pass-QC reads only"/>
+        <param name="proper" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false"
             label="Only count proper pairs"
-            help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" />
+            help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field" />
     </inputs>
     <outputs>
-        <data name="output" metadata_source="input" format_source="input" />
+        <data name="output" format_source="input" metadata_source="input" />
     </outputs>
     <tests>
         <test>
             <param name="input" value="multiCov1.bed" ftype="bed" />
             <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/>
             <param name="q" value="1"/>
-            <param name="split" value="False"/>
+            <param name="split" value=""/>
             <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.
 
-
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 multiIntersectBed.xml
--- a/multiIntersectBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/multiIntersectBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,36 +1,35 @@
-<tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@WRAPPER_VERSION@">
+<tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@+galaxy1">
     <description>identifies common intervals among multiple interval files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools multiinter
-        $header
-        $cluster
-        -filler "${filler}"
-        $empty.empty_selector
-        @GENOME_FILE_UNION@
+    <command><![CDATA[
+bedtools multiinter
+$header
+$cluster
+-filler '${filler}'
+$empty.empty_selector
+@GENOME_FILE_UNION@
 
-        #if str($tag.tag_select) == "tag":
-            #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
-            -i "${files}"
-        #else:
-            -i
-            #for $file in $tag.beds:
-                "${file.input}"
-            #end for
-            -names
-            #for $file in $tag.beds:
-                "{$file.custom_name}"
-            #end for
-        #end if
-
-        > '$output'
-]]>
-    </command>
+#if str($tag.tag_select) == "tag":
+    -i
+    #for $file in $tag.inputs
+        '$file'
+    #end for
+#else:
+    -i
+    #for $file in $tag.beds:
+        '${file.input}'
+    #end for
+    -names
+    #for $file in $tag.beds:
+        '{$file.custom_name}'
+    #end for
+#end if
+> '$output'
+    ]]></command>
     <inputs>
         <conditional name="tag">
             <param name="tag_select" type="select" label="Sample name">
@@ -38,18 +37,17 @@
                 <option value="custom">Enter custom name per file</option>
             </param>
             <when value="tag">
-                <param name="inputs" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
+                <param name="inputs" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
             </when>
             <when value="custom">
                 <repeat name="beds" title="Add BED files" min="2" >
-                    <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
+                    <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
                     <param name="custom_name" type="text" area="false" label="Custom sample name" />
                 </repeat>
             </when>
         </conditional>
-        <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue=""
-            label="Invoke Ryan Layers's clustering algorithm"
-            help="(-cluster)" />
+        <param argument="-cluster" type="boolean" truevalue="-cluster" falsevalue="" checked="false"
+            label="Invoke Ryan Layers's clustering algorithm" />
         <conditional name="empty">
             <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
                 <option value="-empty">Yes</option>
@@ -60,14 +58,13 @@
             </when>
             <when value="" />
         </conditional>
-        <param name="filler" type="text" value="N/A"
+        <param argument="-filler" type="text" value="N/A"
             label="Text to use for no-coverage value"
-            help="Can be 0.0, N/A, - or any other value. (-filler)" />
+            help="Can be 0.0, N/A, - or any other value" />
         <expand macro="print_header" />
-
     </inputs>
     <outputs>
-        <data format="bed" name="output" />
+        <data name="output" format="bed" />
     </outputs>
     <tests>
         <test>
@@ -92,8 +89,7 @@
             <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files.
@@ -179,7 +175,6 @@
 
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 nucBed.xml
--- a/nucBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/nucBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,40 +1,38 @@
-<tool id="bedtools_nucbed" name="bedtools NucBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_nucbed" name="bedtools NucBed" version="@TOOL_VERSION@">
     <description>profile the nucleotide content of intervals in a FASTA file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools nuc
-        $s
-        $seq
-        #if str($pattern):
-            -pattern '$pattern'
-            $C
-        #end if
-        -fi '$fasta'
-        -bed '$input'
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools nuc
+$s
+$seq
+#if str($pattern):
+    -pattern '$pattern'
+    $C
+#end if
+-fi '$fasta'
+-bed '$input'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param format="fasta" name="fasta" type="data" label="FASTA file"/>
+        <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file"/>
 
-        <param argument="-s" type="boolean" checked="false" truevalue="-s" falsevalue=""
+        <param argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
             label="Profile the sequence according to strand" />
-        <param argument="-seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
+        <param argument="-seq" type="boolean" truevalue="-seq" falsevalue="" checked="false"
             label="Print the extracted sequence" />
         <param argument="-pattern" type="text" label="Report the number of times a user-defined sequence is observed" help="Case-sensitive by default">
             <validator type="regex" message="Sequence should only contain letters.">^[A-Za-z]*$</validator>
         </param>
-        <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue=""
+        <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false"
             label="Ignore case when matching -pattern"/>
     </inputs>
     <outputs>
-        <data format="tabular" name="output" />
+        <data name="output" format="tabular" />
     </outputs>
     <tests>
         <test>
@@ -56,14 +54,12 @@
             <output name="output" file="nucBed_result3.bed" ftype="tabular" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Profiles the nucleotide content of intervals in a fasta file.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 overlapBed.xml
--- a/overlapBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/overlapBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,26 +1,24 @@
-<tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@TOOL_VERSION@">
     <description>computes the amount of overlap from two intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools overlap
-        -i '$input'
-        -cols $cols
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools overlap
+-i '$input'
+-cols $cols
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param name="cols" type="data_column" multiple="True" data_ref="input"
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="cols" type="data_column" data_ref="input" multiple="true"
             label="Specify the columns for the starts and ends of the features for which you’d like to compute the overlap/distance"
             help="The columns must be listed in the following order: start1,end1,start2,end2" />
     </inputs>
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" label="Overlap of ${input.name}"/>
+        <data name="output" format_source="input" metadata_source="input" label="Overlap of ${input.name}"/>
     </outputs>
     <tests>
         <test>
@@ -29,14 +27,12 @@
             <output name="output" file="overlapBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 overlap computes the amount of overlap (in the case of positive values) or distance (in the case of negative values) between feature coordinates occurring on the same input line and reports the result at the end of the same line. In this way, it is a useful method for computing custom overlap scores from the output of other BEDTools.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 randomBed.xml
--- a/randomBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/randomBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,30 +1,28 @@
-<tool id="bedtools_randombed" name="bedtools RandomBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@">
     <description>generate random intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools random
-        -g @GENOME_FILE@
-        -l $length
-        -n $intervals
-        #if str($seed.seed_choose) == "True":
-            -seed $seed.seed
-        #end if
-        > "$output"
-]]>
-    </command>
+    <command><![CDATA[
+bedtools random
+-g @GENOME_FILE@
+-l $length
+-n $intervals
+#if str($seed.seed_choose) == "True":
+    -seed $seed.seed
+#end if
+> '$output'
+    ]]></command>
     <inputs>
         <expand macro="input_conditional_genome_file" />
-        <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" />
-        <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" />
+        <param name="length" argument="-l" type="integer" value="100" label="The length of the intervals to generate" />
+        <param name="intervals" argument="-n" type="integer" value="1000000" label="The number of intervals to generate" />
         <expand macro="seed" />
     </inputs>
     <outputs>
-        <data format="bed" name="output" />
+        <data name="output" format="bed" />
     </outputs>
     <tests>
         <test>
@@ -41,14 +39,12 @@
             </output>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (-n) and the size (-l) of the intervals that should be generated.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 reldist.xml
--- a/reldist.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/reldist.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,27 +1,25 @@
-<tool id="bedtools_reldistbed" name="bedtools ReldistBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_reldistbed" name="bedtools ReldistBed" version="@TOOL_VERSION@">
     <description>calculate the distribution of relative distances</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools reldist
-        -a '$inputA'
-        -b '$inputB'
-        $detail
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools reldist
+-a '$inputA'
+-b '$inputB'
+$detail
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param name="detail" type="boolean" checked="false" truevalue="-detail" falsevalue=""
-            label="Instead of a summary, report the relative distance for each interval in A" help="(-detail)" />
+        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
+        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param argument="-detail" type="boolean" truevalue="-detail" falsevalue="" checked="false"
+            label="Instead of a summary, report the relative distance for each interval in A" />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label="Relalative distance of ${inputA.name} and ${inputB.name}"/>
+        <data name="output" format_source="inputA" metadata_source="inputA" label="Relalative distance of ${inputA.name} and ${inputB.name}"/>
     </outputs>
     <tests>
         <test>
@@ -30,8 +28,7 @@
             <output name="output" file="reldistBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Traditional approaches to summarizing the similarity between two sets of genomic intervals are based upon the number or proportion of intersecting intervals. However, such measures are largely blind to spatial correlations between the two sets where, dpesite consistent spacing or proximity, intersections are rare (for example, enhancers and transcription start sites rarely overlap, yet they are much closer to one another than two sets of random intervals). Favorov et al proposed a relative distance metric that describes distribution of relative distances between each interval in one set nd the two closest intervals in another set (see figure above). If there is no spatial correlation between the two sets, one would expect the relative distances to be uniformaly distributed among the relative distances ranging from 0 to 0.5. If, however, the intervals tend to be much closer than expected by chance, the distribution of observed relative distances would be shifted towards low relative distance values (e.g., the figure below).
@@ -41,8 +38,7 @@
 .. class:: infomark
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1371/journal.pcbi.1002529</citation>
     </expand>
diff -r 87ee588b3d45 -r dde39ba9c031 shuffleBed.xml
--- a/shuffleBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/shuffleBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,68 +1,68 @@
-<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@">
     <description>randomly redistrubute intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools shuffle
-        -g @GENOME_FILE@
-        -i '$inputA'
-        $bedpe
-        #if str($seed.seed_choose) == "True":
-            -seed $seed.seed
-        #end if
-        #if str($add_bed.add_bed_select) == "not_be":
-            -excl $add_bed.excl
-            -f $add_bed.overlap
-        #elif str($add_bed.add_bed_select) == "be":
-            -incl $add_bed.incl
-        #end if
-        $chrom
-        $chromfirst
-        $no_overlap
-        $allow_beyond
-        -maxTries $maxtries
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools shuffle
+-g @GENOME_FILE@
+-i '$inputA'
+$bedpe
+#if str($seed.seed_choose) == "True":
+    -seed $seed.seed
+#end if
+#if str($add_bed.add_bed_select) == "not_be":
+    -excl $add_bed.excl
+    #if str($add_bed.overlap)
+        -f $add_bed.overlap
+    #end if
+#elif str($add_bed.add_bed_select) == "be":
+    -incl $add_bed.incl
+#end if
+$chrom
+$chromfirst
+$no_overlap
+$allow_beyond
+-maxTries $maxtries
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" />
+        <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param argument="-bedpe" type="boolean" truevalue="-bedpe" falsevalue="" checked="false" label="The file is in BEDPE format" />
         <expand macro="input_conditional_genome_file" />
-        <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue=""
+        <param argument="-chrom" type="boolean" truevalue="-chrom" falsevalue="" checked="false"
             label="Keep features in the input file on the same chromosome"
-            help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" />
+            help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen." />
         <expand macro="seed" />
         <conditional name="add_bed">
             <param name="add_bed_select" type="select" label="Choose an additional BED file">
-                <option value="no" selected="True">No additional BED file</option>
+                <option value="no" selected="true">No additional BED file</option>
                 <option value="not_be">Coordinates in which features from -i should not be placed?</option>
                 <option value="be">coordinates in which features from -i should be placed?</option>
             </param>
             <when value="no" />
             <when value="not_be">
-                <param name="excl" type="data" format="bed" label="Choose File" />
-                <expand macro="overlap" />
+                <param argument="-excl" type="data" format="bed" label="Choose File" />
+                <expand macro="fraction" name="overlap" argument="-f" label="Maximum overlap (as a fraction of the -i feature) with an -excl feature that is tolerated before searching for a new, randomized locus" />
             </when>
             <when value="be">
-                <param name="incl" type="data" format="bed" label="Choose File" />
+                <param argument="-incl" type="data" format="bed" label="Choose File" />
             </when>
         </conditional>
-        <param name="chromfirst" type="boolean" checked="False" truevalue="-chromFirst" falsevalue="" 
+        <param name="chromfirst" argument="-chromFirst" type="boolean" truevalue="-chromFirst" falsevalue="" checked="false"
             label="Choose chromosome first"
-            help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size. (-chromFirst)" />
-        <param name="maxtries" type="integer" value="1000"
-            label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" />
-        <param name="no_overlap" type="boolean" checked="False" truevalue="-noOverlapping" falsevalue=""
-            label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" />
-        <param name="allow_beyond" type="boolean" checked="False" truevalue="-allowBeyondChromEnd" falsevalue=""
-            label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" />
+            help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size." />
+        <param name="maxtries" argument="-maxTries" type="integer" value="1000"
+            label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" />
+        <param name="no_overlap" argument="-noOverlapping" type="boolean" truevalue="-noOverlapping" falsevalue="" checked="false"
+            label="Don’t allow shuffled intervals to overlap" />
+        <param name="allow_beyond" argument="-allowBeyondChromEnd" type="boolean" truevalue="-allowBeyondChromEnd" falsevalue="" checked="false"
+            label="Allow the original the length of the original records to extebd beyond the length of the chromosome" />
     </inputs>
     <outputs>
-        <data format="bed" name="output" />
+        <data name="output" format="bed" />
     </outputs>
     <tests>
         <test>
@@ -102,8 +102,7 @@
             <output name="output" file="shuffleBed_result4.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” @STD_BEDTOOLS_INPUT_LABEL@ file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the significance of associations of one feature with another.
@@ -111,7 +110,6 @@
 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 slopBed.xml
--- a/slopBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/slopBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,41 +1,39 @@
-<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@">
     <description>adjust the size of intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools slop
-        $pct
-        $strand
-        -g @GENOME_FILE@
-        -i '$inputA'
-        #if $addition.addition_select == 'b':
-            -b $addition.b
-        #else:
-            -l $addition.l
-            -r $addition.r
-        #end if
-        $header
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools slop
+$pct
+$strand
+-g @GENOME_FILE@
+-i '$inputA'
+#if $addition.addition_select == 'b':
+    -b $addition.b
+#else:
+    -l $addition.l
+    -r $addition.r
+#end if
+$header
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
         <expand macro="input_conditional_genome_file" />
-        <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
+        <param argument="-pct" type="boolean" truevalue="-pct" falsevalue="" checked="false"
             label="Define -l and -r as a fraction of the feature’s length"
             help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
             label="Define -l and -r based on strand"
             help="If used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
         <expand macro="addition" />
         <expand macro="print_header" />
     </inputs>
     <outputs>
-        <data format="bed" name="output"/>
+        <data name="output" format="bed" />
     </outputs>
     <tests>
         <test>
@@ -56,8 +54,7 @@
             <output name="output" file="slopBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size).
@@ -67,8 +64,8 @@
 .. class:: warningmark
 
 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig.
+
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 sortBed.xml
--- a/sortBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/sortBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,20 +1,18 @@
-<tool id="bedtools_sortbed" name="bedtools SortBED" version="@WRAPPER_VERSION@">
+<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@">
     <description>order the intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        sortBed
-            -i '$input'
-            $option
-            > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+sortBed
+-i '$input'
+$option
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" />
         <param name="option" type="select" label="Sort by">
             <!-- sort -k 1,1 -k2,2 -n a.bed -->
             <option value="">chromosome, then by start position (asc)</option>
@@ -27,7 +25,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/>
+        <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
     </outputs>
     <tests>
         <test>
@@ -36,8 +34,7 @@
             <output name="output" file="sortBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Sorts a feature file by chromosome and other criteria.
@@ -50,7 +47,6 @@
 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 spacingBed.xml
--- a/spacingBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/spacingBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,22 +1,20 @@
-<tool id="bedtools_spacingbed" name="bedtools SpacingBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_spacingbed" name="bedtools SpacingBed" version="@TOOL_VERSION@">
     <description>reports the distances between features</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools spacing
-        -i '$input'
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools spacing
+-i '$input'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
+        <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
     </inputs>
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" label="Spaces between intervals of ${input}"/>
+        <data name="output" format_source="input" metadata_source="input" label="Spaces between intervals of ${input}"/>
     </outputs>
     <tests>
         <test>
@@ -24,15 +22,12 @@
             <output name="output" file="spacingBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Report the spacing between intervals in a file.
 
-
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 subtractBed.xml
--- a/subtractBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/subtractBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,34 +1,32 @@
-<tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@TOOL_VERSION@">
     <description>remove intervals based on overlaps</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools subtract
-        $strand
-        -a '$inputA'
-        -b '$inputB'
-        -f $overlap
-        $removeIfOverlap
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools subtract
+$strand
+-a '$inputA'
+-b '$inputB'
+@OVERLAP@
+$removeIfOverlap
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="strand2" />
         <expand macro="overlap" />
         <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
-            <option value="" selected="True">Dont Remove entire feature on overlap</option>
-            <option value="-A">Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed</option>
-            <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature)</option>
+            <option value="" selected="true">Don't Remove entire feature on overlap</option>
+            <option value="-A">Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed (-A)</option>
+            <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature) (-N)</option>
         </param>
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA"/>
+        <data name="output" format_source="inputA" metadata_source="inputA"/>
     </outputs>
     <tests>
         <test>
@@ -49,8 +47,7 @@
             <output name="output" file="subtractBed_result3.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.
@@ -58,7 +55,6 @@
 .. image:: $PATH_TO_IMAGES/subtract-glyph.png
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 tagBed.xml
--- a/tagBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/tagBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,38 +1,38 @@
-<tool id="bedtools_tagbed" name="bedtools TagBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@+galaxy1">
     <description>tag BAM alignments based on overlaps with interval files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        #set files = '" "'.join( [ str( $file ) for $file in $inputB ] )
-        bedtools tag
-        -i "${inputA}"
-        -files "${files}"
-        -f $overlap
-        $strand
-        -tag "${tag}"
-        $field
-        > "${output}"
-]]>
-    </command>
+    <command><![CDATA[
+bedtools tag
+-i '${inputA}'
+-files
+#for $file in $inputB
+    '$file'
+#end for
+@OVERLAP@
+$strand
+-tag '${tag}'
+$field
+> '${output}'
+    ]]></command>
     <inputs>
-        <param name="inputA" format="bam" type="data" label="BAM file"/>
-        <param name="inputB" format="@STD_BEDTOOLS_INPUTS@" multiple="True" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
+        <param name="inputA" argument="-i" type="data" format="bam" label="BAM file"/>
+        <param name="inputB" argument="-files" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
         <expand macro="strand2" />
-        <expand macro="overlap" />
-        <param name="tag" type="text" value="YB" label="Specify the tag to use" />
+        <expand macro="overlap" fracof="the alignment"/>
+        <param argument="-tag" type="text" value="YB" label="Specify the tag to use" />
         <param name="field" type="select" label="Field from the annotation files to populate tags?">
-            <option value="-labels" selected="True">Labels</option>
+            <option value="-labels" selected="true">Labels</option>
             <option value="-scores">Scores</option>
             <option value="-names">Names</option>
             <option value="-labels -intervals">Intervals</option>
         </param>
     </inputs>
     <outputs>
-        <data format="bam" name="output"/>
+        <data name="output" format="bam" />
     </outputs>
     <tests>
         <test>
@@ -42,14 +42,12 @@
             <output name="output" file="tagBed_result1.bam" ftype="bam" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Annotates a BAM file based on overlaps with multiple @STD_BEDTOOLS_INPUT_LABEL@ files on the intervals in an input bam file
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 test-data/coverageBed_result3_f1r.bed
--- a/test-data/coverageBed_result3_f1r.bed	Mon Dec 17 14:23:31 2018 -0500
+++ b/test-data/coverageBed_result3_f1r.bed	Mon Apr 29 05:55:48 2019 -0400
@@ -1,4 +1,4 @@
-chr1	10	20	0	0	10	0.0000000
-chr1	20	30	0	0	10	0.0000000
-chr1	30	40	0	0	10	0.0000000
+chr1	10	20	1	10	10	1.0000000
+chr1	20	30	1	10	10	1.0000000
+chr1	30	40	1	10	10	1.0000000
 chr1	100	200	1	100	100	1.0000000
diff -r 87ee588b3d45 -r dde39ba9c031 unionBedGraphs.xml
--- a/unionBedGraphs.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/unionBedGraphs.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,34 +1,34 @@
-<tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@WRAPPER_VERSION@">
+<tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@TOOL_VERSION@">
     <description>combines coverage intervals from multiple BEDGRAPH files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-    unionBedGraphs
-        $header
-        -filler "${filler}"
-        $empty.empty_selector
-        @GENOME_FILE_UNION@
+    <command><![CDATA[
+unionBedGraphs
+$header
+-filler '${filler}'
+$empty.empty_selector
+@GENOME_FILE_UNION@
 
-        #if str($tag.tag_select) == "tag":
-            #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
-            -i "${files}"
-        #else:
-            -i
-            #for $bg in $tag.bedgraphs:
-                "${bg.input}"
-            #end for
-            -names
-            #for $bg in $tag.bedgraphs:
-                "${bg.custom_name}"
-            #end for
-        #end if
-        > "${output}"
-]]>
-    </command>
+#if str($tag.tag_select) == "tag":
+    -i
+    #for $file in $tag.inputs:
+        '${file}'
+    #end for
+#else:
+    -i
+    #for $bg in $tag.bedgraphs:
+        '${bg.input}'
+    #end for
+    -names
+    #for $bg in $tag.bedgraphs:
+        '${bg.custom_name}'
+    #end for
+#end if
+> '${output}'
+    ]]></command>
     <inputs>
         <conditional name="tag">
             <param name="tag_select" type="select" label="Sample name">
@@ -36,12 +36,12 @@
                 <option value="custom">Enter custom name per file</option>
             </param>
             <when value="tag">
-                <param name="inputs" format="bedgraph" type="data" multiple="True" label="BedGraph files" />
+                <param name="inputs" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph files" />
             </when>
             <when value="custom">
-                <repeat name="bedgraphs" title="Add BedGraph files" min="2" >
-                    <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" />
-                    <param name="custom_name" type="text" area="false" label="Custom sample name" />
+                <repeat name="bedgraphs" title="Add BedGraph files" min="2">
+                    <param name="input" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph file" />
+                    <param name="custom_name" argument="-names" type="text" area="false" label="Custom sample name" />
                 </repeat>
             </when>
         </conditional>
@@ -55,9 +55,9 @@
             </when>
             <when value="" />
         </conditional>
-        <param name="filler" type="text" value="N/A"
+        <param argument="-filler" type="text" value="N/A"
             label="Text to use for no-coverage value"
-            help="Can be 0.0, N/A, - or any other value. (-filler)" />
+            help="Can be 0.0, N/A, - or any other value" />
         <expand macro="print_header" />
     </inputs>
     <outputs>
@@ -105,8 +105,7 @@
             <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
@@ -229,7 +228,6 @@
     chr1   600    700    0         0.43
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 87ee588b3d45 -r dde39ba9c031 windowBed.xml
--- a/windowBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/windowBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,74 +1,71 @@
-<tool id="bedtools_windowbed" name="bedtools WindowBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_windowbed" name="bedtools WindowBed" version="@TOOL_VERSION@">
     <description>find overlapping intervals within a window around an interval</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools window
-        #if $inputA.is_of_type('bam'):
-            -abam '$inputA'
-        #else:
-            -a '$inputA'
-        #end if
-        -b '$inputB'
-        $bed
-        $strandB
-        #if $addition.addition_select == 'window':
-            -w $addition.w
-        #elif $addition.addition_select == 'lr':
-            -l $addition.l
-            -r $addition.r
-        #end if
-        $original
-        $number
-        $nooverlaps
-        $header
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools window
+#if $inputA.is_of_type('bam'):
+    -abam '$inputA'
+#else:
+    -a '$inputA'
+#end if
+-b '$inputB'
+$bed
+$strandB
+#if $addition.addition_select == 'window':
+    -w $addition.w
+#elif $addition.addition_select == 'lr':
+    -l $addition.l
+    -r $addition.r
+#end if
+$original
+$number
+$nooverlaps
+$header
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param name="bed" type="boolean" checked="false" truevalue="-bed" falsevalue=""
-            label="When using BAM input, write output as BED. The default is to write output in BAM when using a bam file"
-            help="(-bed)" />
+        <param name="inputA" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
+        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
+            label="When using BAM input, write output as BED. The default is to write output in BAM when using a BAM file" />
         <conditional name="addition">
             <param name="addition_select" type="select" label="Choose what you want to do">
                 <option value="window">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</option>
                 <option value="lr">Add Base pairs **separately** for upstream and downstream of each entry in A when searching for overlaps in B</option>
             </param>
             <when value="window">
-                <param name="w" type="integer" value="1000" label="Base pairs to add upstream and downstream" />
+                <param argument="-w" type="integer" value="1000" label="Base pairs to add upstream and downstream" />
             </when>
             <when value="lr">
-                <param name="l" type="integer" value="1000"
+                <param argument="-l" type="integer" value="1000"
                     label="Base pairs added upstream (left) of each entry in A when searching for overlaps in B"
-                    help="Allows one to create assymetrical “windows”. Default is 1000bp. (-l)" />
-                <param name="r" type="integer" value="1000"
+                    help="Allows one to create assymetrical “windows”. Default is 1000bp." />
+                <param argument="-r" type="integer" value="1000"
                     label="Base pairs added downstream (right) of each entry in A when searching for overlaps in B"
-                    help="Allows one to create assymetrical “windows”. Default is 1000bp. (-r)" />
+                    help="Allows one to create assymetrical “windows”. Default is 1000bp." />
             </when>
         </conditional>
         <param name="strandB" type="select" label="Calculation based on strandedness?">
-            <option value="" selected="True">Report any hit in B</option>
+            <option value="" selected="true">Report any hit in B</option>
             <option value="-sm">Only report hits in B that overlap A on the **same** strand</option>
             <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
         </param>
-        <param name="original" type="boolean" checked="false" truevalue="-u" falsevalue=""
+        <param name="original" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false"
             label="Write original A entry once if any overlaps found in B"
-            help="In other words, just report the fact at least one overlap was found in B. (-u)" />
-        <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue=""
+            help="In other words, just report the fact at least one overlap was found in B" />
+        <param name="number" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
             label="For each entry in A, report the number of hits in B"
-            help="Reports 0 for A entries that have no overlap with B (-c)" />
-        <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue=""
-            label="Only report those entries in A that have no overlaps with B" help="(-v)" />
+            help="Reports 0 for A entries that have no overlap with B" />
+        <param name="nooverlaps" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="false"
+            label="Only report those entries in A that have no overlaps with B" />
         <expand macro="print_header" />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
+        <data name="output" format_source="inputA" metadata_source="inputA" />
     </outputs>
     <tests>
         <test>
@@ -92,8 +89,7 @@
             <output name="output" file="windowBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.
@@ -101,7 +97,6 @@
 .. image:: $PATH_TO_IMAGES/window-glyph.png
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>