--- a/read_NVC.xml	Thu Jul 18 11:01:08 2013 -0500
+++ b/read_NVC.xml	Tue Mar 14 10:22:57 2017 -0400
@@ -1,52 +1,69 @@
-<tool id="read_NVC" name="Read NVC">
-	<description>to check the nucleotide composition bias</description>
-	<requirements>
-		<requirement type="package" version="2.15.1">R</requirement>
-		<requirement type="package" version="2.3.7">rseqc</requirement>
-	</requirements>
-	<command interpreter="python"> read_NVC.py -i $input -o output
+<tool id="rseqc_read_NVC" name="Read NVC" version="@WRAPPER_VERSION@">
+    <description>to check the nucleotide composition bias</description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[read_NVC.py --version]]></version_command>
+
+    <command><![CDATA[
+        read_NVC.py
+            --input-file '${input}'
+            --out-prefix output
+            ${nx}
+            --mapq ${mapq}
+    ]]>
+    </command>
 
-		#if $nx
-			-x
-		#end if
-	</command>
-	<inputs>
-		<param name="input" type="data" format="bam,sam" label="input bam/sam file" />
-		<param name="nx" type="boolean" label="Include N,X in NVC plot" value="false" />
-	</inputs>
-	<outputs>
-		<data format="xls" name="outputxls" from_work_dir="output.NVC.xls"/>
-		<data format="r" name="outputr" from_work_dir="output.NVC_plot.r" />
-		<data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" />
-	</outputs>
-	<tests>
-		<test>
-			<param name="input" value="Pairend_nonStrandSpecific_36mer_Human_hg19.bam" />
-			<output name="outputxls" file="readnvcout.NVC.xls" />
-			<output name="outputr" file="readnvcout.NVC_plot.r" />
-			<output name="outputpdf" file="readnvcout.NVC_plot.pdf" />
-		</test>
-	</tests>
-	<help>
-.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
+    <inputs>
+        <expand macro="bam_sam_param" />
+        <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/>
+        <expand macro="mapq_param" />
+        <expand macro="rscript_output_param" />
+    </inputs>
+
+    <outputs>
+        <expand macro="pdf_output_data" filename="output.NVC_plot.pdf" />
+        <expand macro="xls_output_data" filename="output.NVC.xls" />
+        <expand macro="rscript_output_data" filename="output.NVC_plot.r" />
+    </outputs>
 
------
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+            <param name="rscript_output" value="true" />
+            <output name="outputxls" file="output.NVC.xls" />
+            <output name="outputr" file="output.NVC_plot.r" />
+            <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size" />
+        </test>
+    </tests>
 
-About RSeQC
+    <help><![CDATA[
+read_NVC.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.
+This module is used to check the nucleotide composition bias. Due to random priming, certain
+patterns are over represented at the beginning (5'end) of reads. This bias could be easily
+examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all
+reads together, then calculating nucleotide composition for each position of read
+(or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is
+randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
 
-The RSeQC package is licensed under the GNU GPL v3 license.
+NOTE: this program expect a fixed read length
 
 Inputs
 ++++++++++++++
 
 Input BAM/SAM file
-	Alignment file in BAM/SAM format.
+    Alignment file in BAM/SAM format.
 
 Include N,X in NVC plot
-	Plots N and X alongside A, T, C, and G in plot.
+    Plots N and X alongside A, T, C, and G in plot.
 
 Output
 ++++++++++++++
@@ -59,7 +76,16 @@
 3. output.NVC_plot.pdf: NVC plot.
 
 
-.. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/NVC_plot.png
+.. image:: $PATH_TO_IMAGES/NVC_plot.png
+   :height: 600 px
+   :width: 600 px
+   :scale: 80 %
+
+@ABOUT@
 
-	</help>
+]]>
+    </help>
+
+    <expand macro="citations" />
+
 </tool>