--- a/deseq2.xml	Fri Nov 16 14:45:51 2018 -0500
+++ b/deseq2.xml	Tue Dec 04 08:18:46 2018 -0500
@@ -1,11 +1,16 @@
-<tool id="deseq2" name="DESeq2" version="2.11.40.3">
+<tool id="deseq2" name="DESeq2" version="2.11.40.4">
     <description>Determines differentially expressed features from count tables</description>
     <requirements>
-        <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
-        <requirement type="package" version="1.6.0">bioconductor-tximport</requirement>
-        <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement>
-        <requirement type="package" version="0.6.5">r-ggrepel</requirement>
-        <requirement type="package" version="1.0.8">r-pheatmap</requirement>
+        <requirement type="package" version="1.20.0">bioconductor-deseq2</requirement>
+        <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
+        <requirement type="package" version="2.24.0">bioconductor-rhdf5</requirement>
+        <requirement type="package" version="1.8.0">bioconductor-tximport</requirement>
+        <requirement type="package" version="1.32.3">bioconductor-genomicfeatures</requirement>
+        <requirement type="package" version="1.20.2">r-getopt</requirement>
+        <requirement type="package" version="0.8.0">r-ggrepel</requirement>
+        <requirement type="package" version="3.0.1">r-gplots</requirement>
+        <requirement type="package" version="1.0.10">r-pheatmap</requirement>
+        <requirement type="package" version="0.2.20">r-rjson</requirement>
     </requirements>
     <stdio>
         <regex match="Execution halted"
@@ -27,7 +32,7 @@
     <command><![CDATA[
 #if $tximport.tximport_selector == 'tximport':
     #if $tximport.mapping_format.mapping_format_selector == 'gtf':
-        ln -s '$tximport.mapping_format.gtf_file' mapping.gtf &&
+        ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
     #else:
         ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
     #end if
@@ -92,7 +97,7 @@
         -i
         -y $tximport.txtype
         #if $tximport.mapping_format.mapping_format_selector == 'gtf':
-            -x mapping.gtf
+            -x mapping.gff
         #else:
             -x mapping.txt
         #end if
@@ -133,14 +138,14 @@
                 </param>
                 <conditional name="mapping_format">
                     <param name="mapping_format_selector" type="select" label="Gene mapping format">
-                        <option value="gtf" selected="True">GTF</option>
-                        <option value="tabular">Transcript-ID and Gene-ID mapping file</option>
+                        <option value="gtf" selected="True">GTF/GFF3</option>
+                        <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
                     </param>
                     <when value="gtf">
-                        <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/>
+                        <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
                     </when>
                     <when value="tabular">
-                        <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/>
+                        <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
                     </when>
                 </conditional>
             </when>
@@ -190,7 +195,7 @@
             help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
     </inputs>
     <outputs>
-        <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}">
+        <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
             <filter>many_contrasts is False</filter>
             <actions>
                 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
@@ -200,16 +205,16 @@
             <filter>many_contrasts is True</filter>
             <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
         </collection>
-        <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
+        <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
             <filter>pdf == True</filter>
         </data>
-        <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}">
+        <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
             <filter>normCounts == True</filter>
         </data>
-        <data format="tabular" name="rlog_out" label="rLog-Normalized counts file on ${on_string}">
+        <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
             <filter>normRLog == True</filter>
         </data>
-        <data format="tabular" name="vst_out" label="VST-Normalized counts file on ${on_string}">
+        <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
             <filter>normVST == True</filter>
         </data>
     </outputs>
@@ -251,7 +256,7 @@
             </output>
             <output name="deseq_out" >
                 <assert_contents>
-                    <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />
+                    <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
                 </assert_contents>
             </output>
         </test>
@@ -315,7 +320,7 @@
             </output>
             <output name="deseq_out" >
                 <assert_contents>
-                    <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />
+                    <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
                 </assert_contents>
             </output>
         </test>
@@ -339,7 +344,31 @@
             <param name="tabular_file" value="tx2gene.tab"/>
             <output name="deseq_out" >
                 <assert_contents>
-                    <has_text_matching expression="MIR6859-2\t1.1858.*\t-1.5832.*\t1.2956.*\t-1.2219.*\t0.2217.*\t0.8868.*" />
+                    <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
+                </assert_contents>
+            </output>
+        </test>
+        <!--Ensure Sailfish/Salmon input with GFF3 annotation works-->
+        <test expect_num_outputs="1">
+            <repeat name="rep_factorName">
+                <param name="factorName" value="Treatment"/>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Treated"/>
+                    <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Untreated"/>
+                    <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
+                </repeat>
+            </repeat>
+            <param name="pdf" value="False"/>
+            <param name="tximport_selector" value="tximport"/>
+            <param name="txtype" value="sailfish"/>
+            <param name="mapping_format_selector" value="gtf"/>
+            <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
+            <output name="deseq_out" >
+                <assert_contents>
+                    <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
                 </assert_contents>
             </output>
         </test>