--- a/trinity.xml	Mon Aug 28 16:53:46 2017 -0400
+++ b/trinity.xml	Fri Dec 15 07:57:50 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0">
+<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.1">
     <description>de novo assembly of RNA-Seq data</description>
     <macros>
         <import>macros.xml</import>
@@ -20,11 +20,20 @@
                 --seqType fq
             #end if
 
-            #if $inputs.strand.is_strand_specific:
-                --SS_lib_type $inputs.strand.library_type
+            @COMMAND_PAIRED_STRAND_JACCARD@
+
+        #elif $inputs.paired_or_single == "paired_collection"
+            --left ${ ','.join(['"%s"' % x.forward for x in $inputs.pair_input]) }
+
+            --right ${ ','.join(['"%s"' % x.reverse for x in $inputs.pair_input]) }
+
+            #if $inputs.pair_input[0].forward.is_of_type('fasta'):
+                --seqType fa
+            #else:
+                --seqType fq
             #end if
 
-            $inputs.jaccard_clip
+            @COMMAND_PAIRED_STRAND_JACCARD@
 
         #else:
             --single ${ ','.join(['"%s"' % x for x in $inputs.input]) }
@@ -74,27 +83,12 @@
     <inputs>
         <conditional name="inputs">
             <param name="paired_or_single" type="select" label="Paired or Single-end data?">
-                <option value="paired">Paired</option>
-                <option value="single">Single</option>
+                <option value="single">Single-end</option>
+                <option value="paired" selected="true">Paired-end</option>
+                <option value="paired_collection">Paired-end collection</option>
             </param>
-            <when value="paired">
-                <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" 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" 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" argument="--single" multiple="true" type="data" label="Single-end reads" help=""/>
+                <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/>
                 <conditional name="strand">
                     <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                     <when value="false">
@@ -107,6 +101,15 @@
                     </when>
                 </conditional>
             </when>
+            <when value="paired">
+                <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" />
+                <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" />
+                <expand macro="input_paired_strand_jaccard" />
+            </when>
+            <when value="paired_collection">
+                <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/>
+                <expand macro="input_paired_strand_jaccard" />
+            </when>
         </conditional>
 
         <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."/>
@@ -122,20 +125,19 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
+                    <param name="genome_guided_bam" argument="--genome_guided_bam" type="data" format="bam" 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 name="long_reads" argument="--long_reads" type="data" format="fasta" 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>
-        <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /-->
-        <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
+        <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
     </outputs>
     <tests>
         <test>
@@ -156,11 +158,34 @@
             <param name="library_type" value="RF"/>
             <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
         </test>
+        <test>
+            <param name="paired_or_single" value="paired_collection"/>
+            <param name="pair_input">
+                <collection type="list:paired">
+                    <element name="pair1">
+                        <collection type="paired">
+                            <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
+                            <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
+                        </collection>
+                    </element>
+                    <element name="pair2">
+                        <collection type="paired">
+                            <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
+                            <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
+                        </collection>
+                    </element>
+                </collection>
+            </param>
+            <param name="is_strand_specific" value="true"/>
+            <param name="norm" value="true"/>
+            <param name="library_type" value="RF"/>
+            <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
+        </test>
     </tests>
     <help>
-        Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
 
-        .. _Trinity: http://trinityrnaseq.github.io
+.. _Trinity: http://trinityrnaseq.github.io
     </help>
 
     <expand macro="citation" />