--- a/DESeq.xml	Tue Aug 08 15:06:40 2017 -0400
+++ b/DESeq.xml	Tue Nov 07 13:50:32 2017 -0500
@@ -1,10 +1,10 @@
 <tool id="DESeq" name="DESeq2: DESeq" version="1.0.0">
     <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>
@@ -18,46 +18,52 @@
         An R Markdown tool to perform 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[
 
         Rscript '${__tool_directory__}/DESeq_render.R'
 
+
             ## 1. input data
             -e $echo
-            -c $count_files
-            -s $sample_table
-            -p "$design_formula"
+            ##----- code chunk to get file paths and raw file names for a multiple inputs data field ----
+            #set $sep = ''
+            #set $count_file_paths = ''
+            #set $count_file_names = ''
+            #for $count_file in $count_files:
+                #set $count_file_paths += $sep + str($count_file)
+                #set $count_file_names += $sep + str($count_file.name)
+                #set $sep = ','
+            #end for
+            ##----------------- end for getting file names and file paths ------------------------------
+            -P '$count_file_paths'
+            -N '$count_file_names'
+            -S $sample_table
+            -p '$design_formula'
 
             ## 2. output report and report site directory
-		    -o $DESeq
-		    -d $DESeq.files_path
+		    -r $report
+		    -d $report.files_path
+		    -s $sink_message
 		    -w $deseq_workspace
 
-		    ## 3. Rmd templates sitting in the tool directory
-
-		        ## _site.yml and index.Rmd template files
-                -D '${__tool_directory__}/DESeq.Rmd'
+		    ## 3. Rmd templates from the tool directory
+            -t '${__tool_directory__}/DESeq.Rmd'
 
 
 
         ]]>
     </command>
     <inputs>
-        <param type="data" name="count_files" format="tabular" multiple="true" label="Count files from htseq-count" />
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
+               label="Display analysis code in report?"/>
+        <param type="data" name="count_files" format="tabular" multiple="true" label="Count files from htseq-count"/>
         <param type="data" name="sample_table" format="tabular" multiple="false" label="sample table file"
                help="The sample table file contains a table. The first column is the sample name, the second column is
                     the count file name and the rest of columns are treatment columns. The file names in this table have
@@ -72,11 +78,11 @@
                 </valid>
             </sanitizer>
         </param>
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
     </inputs>
     <outputs>
-        <data name="DESeq" format="html" label="DESeq Analysis" />
-        <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis" />
+        <data name="report" format="html" label="DESeq Analysis on ${on_string}"/>
+        <data format="txt" name="sink_message" label="Warnings and Errors on ${on_string}" from_work_dir="warnings_and_errors.txt"/>
+        <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis on ${on_string}"/>
     </outputs>
     <citations>
         <citation>
@@ -94,7 +100,8 @@
         <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}
@@ -110,21 +117,15 @@
             }
         </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>