--- a/trinity.xml	Mon Apr 25 10:02:37 2016 -0400
+++ b/trinity.xml	Tue May 03 10:54:25 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="trinity" name="Trinity" version="2.1.1">
+<tool id="trinity" name="Trinity" version="2.1.1.1">
     <description>de novo assembly of RNA-Seq data</description>
     <requirements>
         <requirement type="package" version="2.1.1">trinity</requirement>
@@ -11,34 +11,37 @@
 
         ## Inputs.
         #if $inputs.paired_or_single == "paired":
-            --left $inputs.left_input --right $inputs.right_input
-            
-            #if $inputs.left_input.is_of_type('fasta'):
+
+            --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) }
+
+            --right ${ ','.join(['"%s"' % x for x in $inputs.right_input]) }
+
+            #if $inputs.left_input[0].is_of_type('fasta'):
                 --seqType fa
             #else:
                 --seqType fq
             #end if
-            
+
             #if $inputs.strand.is_strand_specific:
                 --SS_lib_type $inputs.strand.library_type
             #end if
-            
+
             $inputs.jaccard_clip
 
         #else:
-            --single $inputs.input
-            
-            #if $inputs.input.is_of_type('fasta'):
+            --single ${ ','.join(['"%s"' % x for x in $inputs.input]) }
+
+            #if $inputs.input[0].is_of_type('fasta'):
                 --seqType fa
             #else:
                 --seqType fq
             #end if
-            
+
             #if $inputs.strand.is_strand_specific:
                 --SS_lib_type $inputs.strand.library_type
             #end if
         #end if
-            
+
         $norm
 
         ## Additional parameters.
@@ -58,12 +61,12 @@
             #if $additional_params.guided.genome_guided_min_reads_per_partition:
                 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
             #end if
-            
+
         #end if
 
         ## CPU and butterfly options.
         --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
-        
+
         ## > $trinity_log 2>&1
 
     ]]></command>
@@ -74,8 +77,8 @@
                 <option value="single">Single</option>
             </param>
             <when value="paired">
-                <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
-                <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
+                <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=""/>
                 <conditional name="strand">
                     <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                     <when value="false">
@@ -90,7 +93,7 @@
                 <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"/>
             </when>
             <when value="single">
-                <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/>
+                <param format="fasta,fastqsanger" name="input" 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">
@@ -104,12 +107,12 @@
                 </conditional>
             </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."/>
 
         <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"/>
-            
+
             <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">
                     <option value="no">No</option>
@@ -123,8 +126,8 @@
                     <param name="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" 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"/>
         </section>
     </inputs>
@@ -135,8 +138,8 @@
     <tests>
         <test>
             <param name="paired_or_single" value="paired"/>
-            <param name="left_input" value="reads.left.fq"/>
-            <param name="right_input" value="reads.right.fq"/>
+            <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
+            <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
             <param name="is_strand_specific" value="true"/>
             <param name="norm" value="false"/>
             <param name="library_type" value="RF"/>
@@ -144,8 +147,8 @@
         </test>
         <test>
             <param name="paired_or_single" value="paired"/>
-            <param name="left_input" value="reads.left.fq"/>
-            <param name="right_input" value="reads.right.fq"/>
+            <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
+            <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
             <param name="is_strand_specific" value="true"/>
             <param name="norm" value="true"/>
             <param name="library_type" value="RF"/>
@@ -157,7 +160,7 @@
 
         .. _Trinity: http://trinityrnaseq.github.io
     </help>
-    
+
      <citations>
         <citation type="doi">doi:10.1038/nbt.1883</citation>
     </citations>