--- a/read_NVC.xml	Tue Apr 21 10:27:06 2015 -0400
+++ b/read_NVC.xml	Thu Jul 16 17:43:43 2015 -0400
@@ -1,27 +1,49 @@
-<tool id="rseqc_read_NVC" name="Read NVC" version="2.4">
+<tool id="rseqc_read_NVC" name="Read NVC" version="2.4galaxy1">
     <description>to check the nucleotide composition bias</description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
     <requirements>
-        <requirement type="package" version="3.0.3">R</requirement>
-        <requirement type="package" version="1.7.1">numpy</requirement>
-        <requirement type="package" version="2.4">rseqc</requirement>
+        <expand macro="requirement_package_r" />
+        <expand macro="requirement_package_numpy" />
+        <expand macro="requirement_package_rseqc" />
     </requirements>
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[read_NVC.py --version]]></version_command>
+
     <command>
-        read_NVC.py -i $input -o output $nx
+        read_NVC.py
+            --input-file $input
+            --out-prefix output
+            $nx
+            --mapq $mapq
     </command>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
-        <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
-    </stdio>
+
     <inputs>
-        <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
-        <param name="nx" type="boolean" value="false" truevalue="-x" falsevalue="" label="Include N,X in NVC plot"/>
+        <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
+        <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/>
+        <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
     </inputs>
+
     <outputs>
         <data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" />
         <data format="txt" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
         <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
     </outputs>
-    <help>
+
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <output name="outputxls" file="output.NVC.xls"/>
+            <output name="outputr" file="output.NVC_plot.r"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
 read_NVC.py
 +++++++++++
 
@@ -30,7 +52,7 @@
 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. 
+randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
 
 NOTE: this program expect a fixed read length
 
@@ -57,11 +79,11 @@
 .. image:: http://rseqc.sourceforge.net/_images/NVC_plot.png
    :height: 600 px
    :width: 600 px
-   :scale: 80 %    
+   :scale: 80 %
 
 -----
 
-About RSeQC 
+About RSeQC
 +++++++++++
 
 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.
@@ -71,7 +93,9 @@
 .. image:: http://rseqc.sourceforge.net/_static/logo.png
 
 .. _RSeQC: http://rseqc.sourceforge.net/
-
+]]>
+    </help>
 
-    </help>
+    <expand macro="citations" />
+
 </tool>