--- a/bam2wig.xml	Thu Jul 18 11:01:08 2013 -0500
+++ b/bam2wig.xml	Tue Mar 14 10:22:57 2017 -0400
@@ -1,124 +1,130 @@
-<tool id="bam2wig" name="BAM to Wiggle">
-	<description> 
-		converts all types of RNA-seq data from .bam to .wig 
-	</description>
-	<requirements>
-		<requirement type="package" version="2.15.1">R</requirement>
-		<requirement type="package" version="0.1.18">samtools</requirement>
-		<requirement type="package" version="2.3.7">rseqc</requirement>
-	</requirements>
-	<command interpreter="python"> 
-		samtoolshelper.py /home/nilesh/RSeQC-2.3.3/scripts/bam2wig.py -i $input -s $chromsize -o outfile
+<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@WRAPPER_VERSION@">
+    <description>
+        converts all types of RNA-seq data from .bam to .wig
+    </description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[bam2wig.py --version]]></version_command>
+
+    <command><![CDATA[
+        ln -sf '${input}' 'input.bam' &&
+        ln -sf '${input.metadata.bam_index}' 'input.bam.bai' &&
+        bam2wig.py -i 'input.bam' -s '${chromsize}' -o outfile
 
-		#if str($strand_type.strand_specific) == "pair"
-			-d
-			#if str($strand_type.pair_type) == "sd"
-				'1++,1--,2+-,2-+'
-			#else
-				'1+-,1-+,2++,2--'
-			#end if
-		#end if
+        #if str($strand_type.strand_specific) == "pair"
+            -d
+            #if str($strand_type.pair_type) == "sd"
+                '1++,1--,2+-,2-+'
+            #else
+                '1+-,1-+,2++,2--'
+            #end if
+        #end if
 
-		#if str($strand_type.strand_specific) == "single"
-			-d
-			#if str($strand_type.single_type) == "s"
-				'++,--'
-			#else
-				'+-,-+'
-			#end if
-		#end if
+        #if str($strand_type.strand_specific) == "single"
+            -d
+            #if str($strand_type.single_type) == "s"
+                '++,--'
+            #else
+                '+-,-+'
+            #end if
+        #end if
 
-		#if $wigsum.wigsum_type
-			-t $wigsum.totalwig
-		#end if
+        #if str($wigsum_type.wigsum_type_selector) == "normalize":
+            -t ${wigsum.totalwig}
+        #end if
 
-		#if $skipmultihits
-			-u
-		#end if
-	</command>
-	<inputs>
-		<param name="input" type="data" label="Input .bam File" format="bam" />
-		<param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" />
-		<param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" />
-		<conditional name="wigsum">
-			<param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false">
-			</param>
-			<when value="true">
-				<param name="totalwig" value="0" type="integer" label="specified wigsum" />
-			</when>
-			<when value="false"></when>
-		</conditional>
-		<conditional name="strand_type">
-			<param name="strand_specific" type="select" label="Strand-specific?" value="none">
-				<option value="none">none</option>
-				<option value="pair">Pair-End RNA-seq</option>
-				<option value="single">Single-End RNA-seq</option>
-			</param>
-			<when value="pair">
-				<param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
-					<option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
-					<option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
-				</param>
-			</when>
-			<when value="single">
-				<param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
-					<option value="s">positive --> positive; negative --> negative</option>
-					<option value="d">positive --> negative; negative --> positive</option>
-				</param>
-			</when>
-			<when value="none"></when>
-		</conditional>
-	</inputs>
-	<outputs> 
-		<data format="wig" name="output" from_work_dir="outfile.wig">
-			<filter>strand_type['strand_specific'] == 'none'</filter>
-		</data>
-		<data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig">
-			<filter>strand_type['strand_specific'] != 'none'</filter>
-		</data>
-		<data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig">
-			<filter>strand_type['strand_specific'] != 'none'</filter>
-		</data>
-	</outputs>
-	<tests>
-		<test>
-			<param name="input" value="Pairend_nonStrandSpecific_36mer_Human_hg19.bam" />
-			<param name="chromsize" value="sample.hg19.chrom.sizes.txt" />
-			<param name="skipmultihits" value="false" />
-			<param name="wigsum.wigsum_type" value="false" />
-			<param name="strand_type.strand_specific" value="none" />
-			<output name="output" file="outfile.wig" />
-		</test>
-	</tests>
-	<help>
-.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
+        @MULTIHITS@
+        ]]>
+    </command>
+    <inputs>
+        <expand macro="bam_param" />
+        <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/>
+        <expand macro="multihits_param" />
+        <conditional name="wigsum_type">
+            <param name="wigsum_type_selector" type="select" label="Normalization">
+                <option value="normalize">Normalize to specified sum</option>
+                <option value="raw" selected="true">Do not normalize</option>
+            </param>
+            <when value="normalize">
+                <param name="totalwig" value="" type="integer" label="specified wigsum" help="(--wigsum)"/>
+            </when>
+            <when value="raw"/>
+        </conditional>
+        <expand macro="strand_type_param" />
+    </inputs>
+
+    <outputs>
+        <data format="wig" name="output" from_work_dir="outfile.wig">
+            <filter>strand_type['strand_specific'] == 'none'</filter>
+        </data>
+        <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)">
+            <filter>strand_type['strand_specific'] != 'none'</filter>
+        </data>
+        <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)">
+            <filter>strand_type['strand_specific'] != 'none'</filter>
+        </data>
+    </outputs>
 
------
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="chromsize" value="hg19.chrom.sizes"/>
+            <output name="output" file="testwig.wig"/>
+        </test>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="chromsize" value="hg19.chrom.sizes"/>
+            <param name="multihits_type.multihits_type_selector" value="skipmultihits"/>
+            <param name="multihits_type.mapq" value="20"/>
+            <output name="output" file="testwig.wig"/>
+        </test>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="chromsize" value="hg19.chrom.sizes"/>
+            <param name="strand_specific" value="pair"/>
+            <param name="pair_type" value="sd"/>
+            <output name="outputfwd" file="testwig.Forward.wig"/>
+            <output name="outputrv" file="testwig.Reverse.wig"/>
+        </test>
+    </tests>
 
-About RSeQC
-+++++++++++
+    <help><![CDATA[
+bam2wig.py
+++++++++++
 
-The RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
-
-The RSeQC package is licensed under the GNU GPL v3 license.
+Visualization is the most straightforward and effective way to QC your RNA-seq
+data. For example, change of expression or new splicing can be easily checked
+by visually comparing two RNA-seq tracks using genome browser such as UCSC_,
+IGB_ and IGV_.  `bam2wig.py` converts all types of RNA-seq data from BAM_
+format into wiggle_ format in one-stop.  wiggle_ files can then be easily
+converted into bigwig_.  Bigwig is indexed, binary format of wiggle file, and
+it's particular useful to display large, continuous dataset on genome
+browser.
 
 Inputs
 ++++++++++++++
 
 Input BAM file
-	Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
+    Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
 
 Chromosome size file
-	Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file.
+    Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file.
 
 Specified wigsum (default=none)
-	Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
+    Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
 
 Skip multiple Hit reads
-	skips multiple hit reads or only use uniquely mapped reads
+    skips multiple hit reads or only use uniquely mapped reads
 
 Strand-specific (default=none)
-	How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
+    How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
 
 Outputs
 ++++++++++++++
@@ -126,6 +132,17 @@
 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
 
+@ABOUT@
 
-	</help>
-</tool>
\ No newline at end of file
+.. _UCSC: http://genome.ucsc.edu/index.html
+.. _IGB: http://bioviz.org/igb/
+.. _IGV: http://software.broadinstitute.org/software/igv/
+.. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
+.. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
+.. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
+]]>
+    </help>
+
+    <expand macro="citations" />
+
+</tool>