--- a/trinity.xml	Tue Jul 12 11:36:16 2016 -0400
+++ b/trinity.xml	Wed Jul 27 08:42:10 2016 -0400
@@ -1,11 +1,14 @@
-<tool id="trinity" name="Trinity" version="2.1.1.1">
+<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0">
     <description>de novo assembly of RNA-Seq data</description>
-    <requirements>
-        <requirement type="package" version="2.1.1">trinity</requirement>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
         <requirement type="package" version="1.1.2">bowtie</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
         <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
-    </requirements>
+    </expand>
+    <expand macro="stdio"/>
     <command><![CDATA[
        Trinity
 
@@ -64,6 +67,10 @@
 
         #end if
 
+        #if $additional_params.min_kmer_cov:
+            --min_kmer_cov $additional_params.min_kmer_cov
+        #end if
+
         ## CPU and butterfly options.
         --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
 
@@ -77,29 +84,29 @@
                 <option value="single">Single</option>
             </param>
             <when value="paired">
-                <param format="fasta,fastqsanger" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/>
-                <param format="fasta,fastqsanger" name="right_input" multiple="true" type="data" label="Right/Reverse strand reads" help=""/>
+                <param format="fasta,fastqsanger" argument="--left" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/>
+                <param format="fasta,fastqsanger" argument="--right" name="right_input" multiple="true" type="data" label="Right/Reverse strand reads" help=""/>
                 <conditional name="strand">
                     <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                     <when value="false">
                     </when>
                     <when value="true">
-                        <param name="library_type" type="select" label="Strand-specific Library Type">
+                        <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
                             <option value="FR">Forward-Reverse</option>
                             <option value="RF">Reverse-Forward</option>
                         </param>
                     </when>
                 </conditional>
-                <param name="jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/>
+                <param name="jaccard_clip" argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/>
             </when>
             <when value="single">
-                <param format="fasta,fastqsanger" name="input" multiple="true" type="data" label="Single-end reads" help=""/>
+                <param format="fasta,fastqsanger" name="input" argument="--single" multiple="true" type="data" label="Single-end reads" help=""/>
                 <conditional name="strand">
                     <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                     <when value="false">
                     </when>
                     <when value="true">
-                        <param name="library_type" type="select" label="Strand-specific Library Type">
+                        <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
                             <option value="F">F</option>
                             <option value="R">R</option>
                         </param>
@@ -108,10 +115,10 @@
             </when>
         </conditional>
 
-        <param name="norm" type="boolean" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
+        <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
 
         <section name="additional_params" title="Additional Options" expanded="False">
-            <param name="min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
+            <param name="min_contig_length" argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
 
             <conditional name="guided">
                 <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information">
@@ -121,14 +128,15 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <param format="bam" name="genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
-                    <param name="genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
-                    <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
+                    <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
+                    <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
+                    <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
                 </when>
             </conditional>
 
+            <param format="fasta" name="long_reads" argument="--long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
 
-            <param format="fasta" name="long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
+            <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
         </section>
     </inputs>
     <outputs>
@@ -161,8 +169,5 @@
         .. _Trinity: http://trinityrnaseq.github.io
     </help>
 
-     <citations>
-        <citation type="doi">10.1038/nbt.1883</citation>
-    </citations>
+    <expand macro="citation" />
 </tool>
-