--- a/rseqc_macros.xml	Tue May 03 16:36:57 2016 -0400
+++ b/rseqc_macros.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -1,8 +1,12 @@
 <macros>
 
-    <xml name="requirement_package_r"><requirement type="package" version="3.0.3">R</requirement></xml>
-    <xml name="requirement_package_numpy"><requirement type="package" version="1.7.1">numpy</requirement></xml>
-    <xml name="requirement_package_rseqc"><requirement type="package" version="2.4">rseqc</requirement></xml>
+    <token name="@WRAPPER_VERSION@">2.6.4</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.6.4">rseqc</requirement>
+        </requirements>
+    </xml>
 
     <xml name="stdio">
         <stdio>
@@ -11,32 +15,141 @@
         </stdio>
     </xml>
 
+    <!-- Params -->
+    <xml name="bam_param">
+        <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/>
+    </xml>
+
+    <xml name="bam_sam_param">
+        <param name="input" type="data" label="Input .bam/.sam file" format="bam,sam" help="(--input-file)"/>
+    </xml>
+
+    <xml name="refgene_param">
+        <param name="refgene" type="data" format="bed" label="Reference gene model" help="(--refgene)"/>
+    </xml>
+
+    <xml name="mapq_param">
+        <param name="mapq" type="integer" label="Minimum mapping quality" value="30" help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot; (--mapq)"/>
+    </xml>
+
+    <xml name="readlength_param">
+        <param name="readlength" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length (--read-align-length)"/>
+    </xml>
+
+    <xml name="readnum_param">
+        <param name="readnum" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile (--read-num)"/>
+    </xml>
+
+    <xml name="sample_size_param">
+        <param name="sample_size" type="integer" label="Number of reads sampled from SAM/BAM file (default = 200000)" value="200000" min="1" help="(--sample-size)"/>
+    </xml>
+
+    <xml name="min_intron_param">
+        <param name="min_intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" help="(--min-intron)" />
+    </xml>
+
+    <xml name="layout_param">
+        <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)">
+            <option value="SE" selected="true">Single-end</option>
+            <option value="PE">Paired-end</option>
+        </param>
+    </xml>
+
+    <xml name="strand_type_param">
+        <conditional name="strand_type">
+            <param name="strand_specific" type="select" label="Strand-specific?">
+                <option value="none" selected="true">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)" help="(--strand)">
+                    <option value="sd" selected="true"> 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)" help="(--strand)">
+                    <option value="s" selected="true">positive --> positive; negative --> negative</option>
+                    <option value="d">positive --> negative; negative --> positive</option>
+                </param>
+            </when>
+            <when value="none"></when>
+        </conditional>
+    </xml>
+
+    <xml name="multihits_param">
+        <conditional name="multihits_type">
+            <param name="multihits_type_selector" type="select" label="Reads with multiple hits" help="(--skip-multi-hits)">
+                <option value="use_multihits" selected="true">Count Mutliple Hit Reads</option>
+                <option value="skip_multihits">Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads</option>
+            </param>
+            <when value="skip_multihits">
+                <expand macro="mapq_param" />
+            </when>
+            <when value="use_multihits" />
+        </conditional>
+    </xml>
+
+    <xml name="rscript_output_param">
+        <param name="rscript_output" type="boolean" value="false" label="Output R-Script"
+            help="Output the R-Script used to generate the plots" />
+    </xml>
+
+
+    <!-- Output -->
+
+    <xml name="pdf_output_data" token_filename="output.pdf">
+        <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (pdf)" />
+    </xml>
+
+    <xml name="xls_output_data" token_filename="output.xls">
+        <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (xls)" />
+    </xml>
+
+    <xml name="rscript_output_data" token_filename="output.r">
+        <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (rscript)">
+            <filter>rscript_output</filter>
+        </data>
+    </xml>
+
+    <!-- Command -->
+    <token name="@MULTIHITS@">
+<![CDATA[
+#if str($multihits_type.multihits_type_selector) == "skip_multihits"
+    --skip-multi-hits
+    --mapq=${multihits_type.mapq}
+#end if
+]]>
+    </token>
+
+    <token name="@ABOUT@">
+
+-----
+
+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.
+
+The RSeQC package is licensed under the GNU GPL v3 license.
+
+.. image:: $PATH_TO_IMAGES/logo.png
+
+.. _RSeQC: http://rseqc.sourceforge.net/
+
+
+    </token>
+
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-    @article{wang_rseqc:_2012,
-        title = {{RSeQC}: quality control of {RNA}-seq experiments},
-        volume = {28},
-        issn = {1367-4803, 1460-2059},
-        shorttitle = {{RSeQC}},
-        url = {http://bioinformatics.oxfordjournals.org/content/28/16/2184},
-        doi = {10.1093/bioinformatics/bts356},
-        abstract = {Motivation: RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses. However, QC is a time-consuming and complex task, due to the massive size and versatile nature of RNA-seq data. Therefore, a convenient and comprehensive QC tool to assess RNA-seq quality is sorely needed.
-    Results: We developed the RSeQC package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models. Most modules in RSeQC take advantage of R scripts for visualization, and they are notably efficient in dealing with large BAM/SAM files containing hundreds of millions of alignments.
-    Availability and implementation: RSeQC is written in Python and C. Source code and a comprehensive user's manual are freely available at: http://code.google.com/p/rseqc/.
-    Contact: WL1\{at\}bcm.edu
-    Supplementary Information: Supplementary data are available at Bioinformatics online.},
-        language = {en},
-        number = {16},
-        urldate = {2015-06-30},
-        journal = {Bioinformatics},
-        author = {Wang, Liguo and Wang, Shengqin and Li, Wei},
-        month = aug,
-        year = {2012},
-        pmid = {22743226},
-        pages = {2184--2185},
-    }
-            </citation>
+            <citation type="doi">10.1093/bioinformatics/bts356</citation>
         </citations>
     </xml>
 </macros>