--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DESeq_results.xml	Mon Aug 07 18:10:55 2017 -0400
@@ -0,0 +1,89 @@
+<tool id="DESeq_results" name="DESeq2: Results" version="1.0.0">
+    <requirements>
+        <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="1.1.0">r-stringr</requirement>
+        <requirement type="package" version="0.4.0">r-highcharter</requirement>
+        <requirement type="package" version="0.2">r-dt</requirement>
+        <requirement type="package" version="1.4.2">r-reshape2</requirement>
+        <requirement type="package" version="4.5.6">r-plotly</requirement>
+        <requirement type="package" version="0.2.0.1">r-formattable</requirement>
+        <requirement type="package" version="0.3.5">r-htmltools</requirement>
+    </requirements>
+    <description>
+        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." />
+    </stdio>
+    <command>
+        <![CDATA[
+        ## Add tools to PATH
+        export PATH=/opt/R-3.2.5/bin:\$PATH &&
+
+        Rscript '${__tool_directory__}/DESeq_results_render.R'
+
+            ## 1. input data
+            -e $echo
+            -w $deseq_workspace
+            -c "$contrast_group"
+            -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"
+
+            ## 2. output report and report site directory
+		    -o $deseq_results
+		    -d $deseq_results.files_path
+
+		    ## 3. Rmd templates sitting in the tool directory
+
+		        ## _site.yml and index.Rmd template files
+                -D '${__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?" />
+    </inputs>
+    <outputs>
+        <data name="deseq_results" format="html" label="DESeq Results" />
+    </outputs>
+</tool>
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