--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DESeq.xml	Tue Aug 08 10:43:18 2017 -0400
@@ -0,0 +1,80 @@
+<tool id="DESeq" name="DESeq2: DESeq" 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>
+        <requirement type="package" version="1.0.8">r-pheatmap</requirement>
+    </requirements>
+    <description>
+        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." />
+    </stdio>
+    <command>
+        <![CDATA[
+
+        Rscript '${__tool_directory__}/DESeq_render.R'
+
+            ## 1. input data
+            -e $echo
+            -c $count_files
+            -s $sample_table
+            -p "$design_formula"
+
+            ## 2. output report and report site directory
+		    -o $DESeq
+		    -d $DESeq.files_path
+		    -w $deseq_workspace
+
+		    ## 3. Rmd templates sitting in the tool directory
+
+		        ## _site.yml and index.Rmd template files
+                -D '${__tool_directory__}/DESeq.Rmd'
+
+
+
+        ]]>
+    </command>
+    <inputs>
+        <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
+                    to be in the same order as the count files uploaded in the previous step. "/>
+        <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula"
+               help="The simplest design formula for differential expression would be ~ condition, where condition
+                     is a column in colData(dds) that specifies which of two (or more groups) the samples belong to">
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="~"/>
+                </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" />
+    </outputs>
+</tool>
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