--- a/DESeq_results.xml	Tue Aug 08 15:06:40 2017 -0400
+++ b/DESeq_results.xml	Tue Nov 07 13:50:32 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="DESeq_results" name="DESeq2: Results" version="1.0.0">
+<tool id="DESeq_results" name="DESeq2: Results" version="2.0.0">
     <requirements>
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
-        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
         <requirement type="package" version="1.2">r-rmarkdown</requirement>
         <requirement type="package" version="1.8.4">r-plyr</requirement>
+        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
         <requirement type="package" version="1.1.0">r-stringr</requirement>
         <requirement type="package" version="0.4.0">r-highcharter</requirement>
         <requirement type="package" version="0.2">r-dt</requirement>
@@ -18,18 +18,11 @@
         An R Markdown tool to display DESeq analysis.
     </description>
     <stdio>
-        <regex match="Execution halted"
-               source="both"
-               level="fatal"
-               description="Execution halted." />
-        <regex match="Error in"
-               source="both"
-               level="fatal"
-               description="An undefined error occured, please check your intput carefully and contact your administrator." />
-        <regex match="Fatal error"
-               source="both"
-               level="fatal"
-               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+        <!--redirecting stderr to a file. "XXX" is used to match with nothing so that tool running won't be interrupted during testing-->
+        <regex match="XXX"
+               source="stderr"
+               level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
     </stdio>
     <command>
         <![CDATA[
@@ -38,53 +31,45 @@
 
             ## 1. input data
             -e $echo
-            -w $deseq_workspace
-            -c "$contrast_group"
-            -t $treatment
-            -k $condition
+            -W $deseq_workspace
+            -C '$contrast_factor'
+            -T '$treatment'
+            -K '$condition'
 
-            #set $groups = []
-            #for $c_group in $clustering_groups
-                #if str($c_group.group)
-                    #set $groups = $groups + [str($c_group.group)]
-                #end if
-            #end for
-            #set $groups = ','.join($groups)
-            -m "$groups"
+            -M '$clustering_factors'
 
             ## 2. output report and report site directory
-		    -o $deseq_results
-		    -d $deseq_results.files_path
+		    -r $report
+            -d $report.files_path
+            -s $sink_message
+            -R $deseq_results
 
 		    ## 3. Rmd templates sitting in the tool directory
-
-		        ## _site.yml and index.Rmd template files
-                -D '${__tool_directory__}/DESeq_results.Rmd'
+            -t '${__tool_directory__}/DESeq_results.Rmd'
 
 
 
         ]]>
     </command>
     <inputs>
-        <param type="data" name="deseq_workspace" format="rdata" multiple="false" label="Workspace from tool DESeq2: DESeq" />
-        <param type="data" name="sample_table" format="tabular" multiple="false" label="Sample table file" />
-        <param type="data_column" name="contrast_group" data_ref="sample_table" use_header_names="true"
-               optional="false"
-               label="Group for result contrast"
-               help=""/>
-        <param type="text" name="treatment" label="Treatment level" />
-        <param type="text" name="condition" label="Condition level" />
-
-        <repeat name="clustering_groups" title="Gene clustering groups" min="1">
-            <param type="data_column" name="group" data_ref="sample_table" use_header_names="true"
-                   optional="false"
-                   label="A phenotype column from the sample table" />
-        </repeat>
-
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
+               label="Display analysis code in report?"/>
+        <param type="data" name="deseq_workspace" format="rdata" multiple="false" optional="false"
+               label="Workspace from tool DESeq2: DESeq"/>
+        <param type="text" name="contrast_factor" label="Factor" optional="false"
+               help="the name of a factor in the design formula"/>
+        <param type="text" name="treatment" label="Treatment level" optional="false"
+               help=" the name of the numerator level for the fold change"/>
+        <param type="text" name="condition" label="Condition level" optional="false"
+               help=" the name of the denominator level for the fold change"/>
+        <param type="text" name="clustering_factors" title="Gene clustering factors" optional="false"
+               label="factors of interest for clustering samples and PCA plot"
+               help="A single factor or multiple factors from the design formula. Multiple factors are separated by comma (,)."/>
     </inputs>
     <outputs>
-        <data name="deseq_results" format="html" label="DESeq Results" />
+        <data format="html" name="report" label="DESeq results report on ${on_string}" />
+        <data format="txt" name="sink_message" label="Warnings and Errors on ${on_string}" from_work_dir="warnings_and_errors.txt"/>
+        <data format="csv" name="deseq_results" label="DESeq results on ${on_string}" from_work_dir="deseq_results.csv" />
     </outputs>
     <citations>
         <citation>
@@ -102,7 +87,8 @@
         <citation type="bibtex">
             @article{allaire2016rmarkdown,
             title={rmarkdown: Dynamic Documents for R, 2016},
-            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
             journal={R package version 0.9},
             volume={6},
             year={2016}
@@ -118,21 +104,15 @@
             }
         </citation>
         <citation>
-            @misc{pheatmap2015,
-            title = {pheatmap: Pretty Heatmaps},
-            author = {Raivo Kolde},
-            year = {2015},
-            note = {R package version 1.0.8},
-            url = {https://CRAN.R-project.org/package=pheatmap},
-            }
-        </citation>
-        <citation>
-            @misc{dt2016,
-            title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
-            author = {Yihui Xie},
-            year = {2016},
-            note = {R package version 0.2},
-            url = {https://CRAN.R-project.org/package=DT},
+            @article{love2014moderated,
+            title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
+            author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
+            journal={Genome biology},
+            volume={15},
+            number={12},
+            pages={550},
+            year={2014},
+            publisher={BioMed Central}
             }
         </citation>
     </citations>