--- a/trinotate.xml	Fri Mar 16 21:52:26 2018 -0400
+++ b/trinotate.xml	Mon Aug 06 06:52:04 2018 -0400
@@ -1,6 +1,6 @@
-<tool id="trinotate" name="Trinotate" version="3.0.1.0">
+<tool id="trinotate" name="Trinotate" version="3.1.1">
     <requirements>
-        <requirement type="package" version="3.0.1">trinotate</requirement>
+        <requirement type="package" version="3.1.1">trinotate</requirement>
         <requirement type="package" version="1.18">gnu-wget</requirement>
     </requirements>
     <stdio>
@@ -8,16 +8,15 @@
     </stdio>
     <version_command>
         <![CDATA[
-            Trinotate version 3.0.1
+            Trinotate version 3.1.1
         ]]>
     </version_command>
     <command><![CDATA[
 
 #if str($cond_download.select_download) == "yes":
-    wget --no-verbose 'https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz' -O Trinotate.sqlite.gz &&
-    gunzip Trinotate.sqlite.gz &&
+    Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate &&
 #else:
-    ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite
+    ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite &&
 #end if
 
 Trinotate Trinotate.sqlite init --gene_trans_map '$gene_trans_map' --transcript_fasta $trinity --transdecoder_pep '$transdecoder' &&
@@ -37,7 +36,7 @@
     Trinotate Trinotate.sqlite LOAD_signalp '$signalp' &&
 #end if
 
-Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_option.pfam_cutoff $report_option.incl_pep $report_option.incl_trans > '$trinotate_out';
+Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_option.pfam_cutoff $report_option.incl_pep $report_option.incl_trans > '$trinotate_out'
 
     ]]></command>
     <inputs>
@@ -48,7 +47,7 @@
         <param name="blastx" type="data" format="tabular" optional="true" label="BLASTX: Transcripts vs Uniprot.SwissProt" help="[optional] NCBI BLAST+ blastx output. Output format: Tabular (standard 12 columns)" />
         <param name="hmmscan" type="data" format="txt" optional="true" label="HMMER hmmscan: Peptides vs PFAM" help="[optional] HMMER hmmscan output: Table of per-domain hits. Output format: Table of per-domain hits (--domtblout)" />
         <param name="tmhmm" type="data" format="tabular" optional="true" label="TMHMM on Peptides" help="[optional]"/>
-        <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" />        
+        <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" />
 
         <conditional name="cond_download">
             <param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database">
@@ -60,7 +59,7 @@
             </when>
             <when value="yes" />
         </conditional>
-        
+
         <section name="report_option" title="Report options" expanded="False">
             <param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations." />
             <param argument="--pfam_cutoff" type="select" label="PFAM cutoff">
@@ -97,6 +96,7 @@
             <param name="tmhmm" ftype="tabular" value="tmhmm.out" />
             <param name="signalp" ftype="tabular" value="signalp.out" />
             <output name="trinotate_out" file="trinotate_annotation_report.xls" />
+            <output name="trinotate_out" file="trinotate_annotation_report.xls" />
         </test>
         <test>
             <param name="trinity" ftype="fasta" value="Trinity.fasta" />
@@ -174,11 +174,6 @@
 
 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
 
-
-Trinotate Pre-generated Resource SQLite database
-
-- You can provide the SQLite database yourself, if Galaxy have trouble to download it : https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz
-
 --------
 
 **Output**