# HG changeset patch
# User mingchen0919
# Date 1502143898 14400
# Node ID f1e4bfc589752ffd7c40c37c19ec611d0520d42d
# Parent  507e408cd6cc3b502c3b1148c2fb92cd79202ab9
Uploaded

diff -r 507e408cd6cc -r f1e4bfc58975 DESeq_visualization.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DESeq_visualization.xml	Mon Aug 07 18:11:38 2017 -0400
@@ -0,0 +1,95 @@
+<tool id="DESeq_visualization" name="DESeq2: Visualization" 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 visualize DESeq analysis results.
+    </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_visualization_render.R'
+
+            ## 1. input data
+            -e $echo
+            -w $deseq_workspace
+            
+            #set $pca_groups = []
+            #for $group in $intgroups_pca
+                #if str($group.intgroup)
+                    #set $pca_groups = $pca_groups + [str($group.intgroup)]
+                #end if
+            #end for
+            #set $pca_groups = ','.join($pca_groups)
+            -p "$pca_groups"
+            
+            #set $mds_groups = []
+            #for $group in $intgroups_mds
+                #if str($group.intgroup)
+                    #set $mds_groups = $mds_groups + [str($group.intgroup)]
+                #end if
+            #end for
+            #set $mds_groups = ','.join($mds_groups)
+            -m "$mds_groups"
+
+            ## 2. output report and report site directory
+		    -o $deseq_visualization
+		    -d $deseq_visualization.files_path
+
+
+		    ## 3. Rmd templates sitting in the tool directory
+
+		        ## _site.yml and index.Rmd template files
+                -D '${__tool_directory__}/DESeq_visualization.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" />
+        <repeat name="intgroups_pca" title="Interest groups for PCA plot" min="1">
+            <param type="data_column" name="intgroup" data_ref="sample_table" use_header_names="true"
+                   optional="false"
+                   label="Interest group for PCA plot"
+                   help=""/>
+        </repeat>
+        <repeat name="intgroups_mds" title="Interest groups for MDS plot" min="1">
+            <param type="data_column" name="intgroup" data_ref="sample_table" use_header_names="true"
+                   optional="false"
+                   label="Interest group for MDS plot"
+                   help=""/>
+        </repeat>
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+    </inputs>
+    <outputs>
+        <data name="deseq_visualization" format="html" label="DESeq Visualization" />
+    </outputs>
+</tool>
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