--- a/trinity.xml	Tue Feb 11 12:22:17 2020 -0500
+++ b/trinity.xml	Fri Mar 19 21:43:30 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@">
+<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy1">
     <description>de novo assembly of RNA-Seq data</description>
     <macros>
         <import>macros.xml</import>
@@ -139,7 +139,7 @@
                         <option value="paired_collection">Paired-end collection</option>
                     </param>
                     <when value="single">
-                        <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/>
+                        <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" 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">
@@ -153,12 +153,12 @@
                         </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" />
+                        <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" />
+                        <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" 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"/>
+                        <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger,fastqsanger.gz" 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>
@@ -170,7 +170,7 @@
                         <option value="unmerged_paired_collection">Paired-end</option>
                     </param>
                     <when value="unmerged_single_collection">
-                        <param name="input" argument="--single" type="data" format="fasta,fastqsanger" label="Single-end reads" help="Elements of collection will NOT be merged"/>
+                        <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Single-end reads" help="Elements of collection will NOT be merged"/>
                         <conditional name="strand">
                             <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                             <when value="false">
@@ -184,7 +184,7 @@
                         </conditional>
                     </when>
                     <when value="unmerged_paired_collection">
-                        <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/>
+                        <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/>
                         <expand macro="input_paired_strand_jaccard" />
                     </when>
                 </conditional>
@@ -224,8 +224,23 @@
             <param name="paired_or_single" value="unmerged_paired_collection"/>
             <param name="pair_input">
                 <collection type="paired">
-                            <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
-                            <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
+                    <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
+                    <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
+                </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_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
+            <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
+        </test>
+        <test>
+            <param name="pool_mode" value="No" />
+            <param name="paired_or_single" value="unmerged_paired_collection"/>
+            <param name="pair_input">
+                <collection type="paired">
+                    <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger" />
+                    <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger"/>
                 </collection>
             </param>
             <param name="is_strand_specific" value="true"/>