# HG changeset patch
# User mingchen0919
# Date 1520558010 18000
# Node ID 405d8fa2f560a2f32da23c96692d853f198ce542
# Parent  157dc02992d90a26e500e270fc24e921405d41de
version 2.2.0

diff -r 157dc02992d9 -r 405d8fa2f560 DESeq.Rmd
--- a/DESeq.Rmd	Tue Feb 27 20:44:34 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,97 +0,0 @@
----
-title: 'DESeq2: Perform DESeq analysis'
-output:
-    html_document:
-      number_sections: true
-      toc: true
-      theme: cosmo
-      highlight: tango
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = as.logical(opt$X_e),
-  error = TRUE
-)
-```
-
-# `DESeqDataSet` object
-
-```{r 'DESeqDataSet object'}
-count_file_paths = strsplit(opt$X_P, ',')[[1]]
-count_file_names = strsplit(opt$X_N, ',')[[1]]
-sample_table = read.table(opt$X_S, header = TRUE)
-row.names(sample_table) = sample_table[,2]
-sample_table = sample_table[count_file_names, ]
-
-## copy count files into OUTPUT_DIR/counts
-dir.create(paste0(OUTPUT_DIR, '/counts'), recursive = TRUE)
-file_copy = file.copy(count_file_paths, paste0(OUTPUT_DIR, '/counts/', count_file_names), overwrite = TRUE)
-
-## DESeqDataSet object
-dds = DESeqDataSetFromHTSeqCount(sampleTable = sample_table,
-                                 directory = paste0(OUTPUT_DIR, '/counts'),
-                                 design = formula(opt$X_p))
-dds
-```
-
-# Pre-filtering the dataset.
-
-We can remove the rows that have 0 or 1 count to reduce object size and increase the calculation speed.
-
-* Number of rows before pre-filtering
-```{r}
-nrow(dds)
-```
-
-* Number of rows after pre-filtering
-```{r}
-dds = dds[rowSums(counts(dds)) > 1, ]
-nrow(dds)
-```
-
-# Peek at data {.tabset}
-
-## Count Data
-
-```{r 'count data'}
-datatable(head(counts(dds), 100), style="bootstrap", 
-          class="table-condensed", options = list(dom = 'tp', scrollX = TRUE))
-```
-
-## Sample Table 
-
-```{r 'sample table'}
-datatable(sample_table, style="bootstrap",
-          class="table-condensed", options = list(dom = 'tp', scrollX = TRUE))
-```
-
-# Sample distance on variance stabilized data {.tabset}
-
-## `rlog` Stabilizing transformation
-
-```{r}
-rld = rlog(dds, blind = FALSE)
-datatable(head(assay(rld), 100), style="bootstrap", 
-          class="table-condensed", options = list(dom = 'tp', scrollX = TRUE))
-```
-
-## Sample distance
-
-```{r}
-sampleDists <- dist(t(assay(rld)))
-sampleDists
-```
-
-# Differential expression analysis
-
-```{r}
-dds <- DESeq(dds)
-```
-
-```{r echo=FALSE}
-# save objects except for opt.
-save(list=ls()[ls() != "opt"], file=opt$X_w)
-```
-
-
diff -r 157dc02992d9 -r 405d8fa2f560 DESeq.xml
--- a/DESeq.xml	Tue Feb 27 20:44:34 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,106 +0,0 @@
-<tool name="DESeq2: Analysis" id='deseq2' version="2.0.1">
-    <description>
-        "some description"
-    </description>
-    <requirements>
-        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
-        <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="1.6">r-rmarkdown</requirement>
-        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
-        <requirement type="package" version="0.2">r-dt</requirement>
-        <requirement type="package" version="1.0.8">r-pheatmap</requirement>
-    </requirements>
-    <stdio>
-        <regex match="XXX" source="stderr" level="warning"
-               description="Check the warnings_and_errors.txt file for more details."/>
-    </stdio>
-    <command><![CDATA[
-        
-
-        Rscript '${__tool_directory__}/DESeq_render.R'
-
-            -e $echo
-
-		    -o $report
-		    -d $report.files_path
-		    -s $sink_message
-		    -t '${__tool_directory__}'
-
-
-		    ##----- 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'
-            -w $deseq_workspace
-
-        
-    ]]></command>
-    <inputs>
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
-               label="Display analysis code in report?"/>
-        <param type="data" name="count_files" format="txt" multiple="true" label="Count files from htseq-count"/>
-        <param type="data" name="sample_table" format="txt" 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>
-    </inputs>
-    <outputs>
-        <data name="report" format="html" label="DESeq Analysis on ${on_string}"/>
-        <data format="txt" name="sink_message" label="Warnings and Errors on"
-              from_work_dir="warnings_and_errors.txt"/>
-        <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis on ${on_string}"/>
-    </outputs>
-    <citations>
-        <citation type="bibtex">
-            @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>
-        <citation type="bibtex"><![CDATA[
-            @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},
-            journal={R package version 0.9},
-            volume={6},
-            year={2016}
-            }
-        ]]></citation>
-        <citation type="bibtex"><![CDATA[
-            @book{xie2015dynamic,
-            title={Dynamic Documents with R and knitr},
-            author={Xie, Yihui},
-            volume={29},
-            year={2015},
-            publisher={CRC Press}
-            }
-        ]]></citation>
-    </citations>
-</tool>
diff -r 157dc02992d9 -r 405d8fa2f560 DESeq_render.R
--- a/DESeq_render.R	Tue Feb 27 20:44:34 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-##============ Sink warnings and errors to a file ==============
-## use the sink() function to wrap all code within it.
-##==============================================================
-zz = file('warnings_and_errors.txt')
-sink(zz)
-sink(zz, type = 'message')
-
-#------------import libraries--------------------
-options(stringsAsFactors = FALSE)
-
-library(getopt)
-library(rmarkdown)
-library(DESeq2)
-library(pheatmap)
-library(DT)
-#------------------------------------------------
-
-
-#------------get arguments into R--------------------
-# getopt_specification_matrix(extract_short_flags('')) %>%
-#   write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
-
-
-spec_matrix = as.matrix(
-  data.frame(stringsAsFactors=FALSE,
-              long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_P", "X_N",
-                             "X_S", "X_p", "X_w"),
-             short_flags = c("e", "o", "d", "s", "t", "P", "N", "S", "p", "w"),
-     argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
-         data_type_flags = c("character", "character", "character", "character",
-                             "character", "character", "character",
-                             "character", "character", "character")
-  )
-)
-opt = getopt(spec_matrix)
-#----------------------------------------------------
-
-
-#-----------using passed arguments in R 
-#           to define system environment variables---
-do.call(Sys.setenv, opt[-1])
-#----------------------------------------------------
-
-#---------- often used variables ----------------
-# OUTPUT_DIR: path to the output associated directory, which stores all outputs
-# TOOL_DIR: path to the tool installation directory
-# RMD_NAME: name of Rmd file to be rendered
-# OUTPUT_REPORT: path to galaxy output report
-OUTPUT_DIR = opt$X_d
-TOOL_DIR =   opt$X_t
-RMD_NAME = 'DESeq.Rmd'
-OUTPUT_REPORT = opt$X_o
-
-# create the output associated directory to store all outputs
-dir.create(OUTPUT_DIR, recursive = TRUE)
-
-#-----------------render Rmd--------------
-render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
-#------------------------------------------
-
-#==============the end==============
-
-
-##--------end of code rendering .Rmd templates----------------
-sink()
-##=========== End of sinking output=============================
\ No newline at end of file
diff -r 157dc02992d9 -r 405d8fa2f560 DESeq_results.Rmd
--- a/DESeq_results.Rmd	Tue Feb 27 20:44:34 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
----
-title: 'DESeq2: Results'
-output:
-    html_document:
-      number_sections: true
-      toc: true
-      theme: cosmo
-      highlight: tango
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = as.logical(opt$X_e),
-  error = TRUE
-)
-```
-
-
-```{r eval=TRUE}
-# Import workspace
-# fcp = file.copy(opt$X_W, "deseq.RData")
-load(opt$X_W)
-```
-
-# Results {.tabset}
-
-## Result table
-
-```{r}
-cat('--- View the top 100 rows of the result table ---')
-res <- results(dds, contrast = c(opt$X_C, opt$X_T, opt$X_K))
-write.csv(as.data.frame(res), file = opt$X_R)
-res_df = as.data.frame(res)[1:100, ]
-datatable(res_df, style="bootstrap", filter = 'top',
-          class="table-condensed", options = list(dom = 'tp', scrollX = TRUE))
-```
-
-## Result summary
-
-```{r}
-summary(res)
-```
-
-
-# MA-plot {.tabset}
-
-
-
-```{r}
-cat('--- Shrinked with Bayesian procedure ---')
-plotMA(res)
-```
-
-
-# Histogram of p values
-
-```{r}
-hist(res$pvalue[res$baseMean > 1], breaks = 0:20/20,
-     col = "grey50", border = "white", main = "",
-     xlab = "Mean normalized count larger than 1")
-```
-
-
-# Visualization {.tabset}
-## Gene clustering
-
-```{r}
-clustering_groups = strsplit(opt$X_M, ',')[[1]]
-
-topVarGenes <- head(order(rowVars(assay(rld)), decreasing = TRUE), 20)
-mat  <- assay(rld)[ topVarGenes, ]
-mat  <- mat - rowMeans(mat)
-annotation_col <- as.data.frame(colData(rld)[, clustering_groups])
-colnames(annotation_col) = clustering_groups
-rownames(annotation_col) = colnames(mat)
-pheatmap(mat, annotation_col = annotation_col)
-```
-
-## Sample-to-sample distance
-
-```{r}
-sampleDistMatrix <- as.matrix( sampleDists )
-colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
-pheatmap(sampleDistMatrix,
-         clustering_distance_cols = sampleDists,
-         col = colors)
-```
-
-## PCA plot 
-
-```{r}
-plotPCA(rld, intgroup = clustering_groups)
-```
-
-## MDS plot {.tabset}
-
-### Data table
-```{r}
-mds <- as.data.frame(colData(rld))  %>%
-         cbind(cmdscale(sampleDistMatrix))
-knitr::kable(mds)
-```
-
-### Plot
-```{r}
-ggplot(mds, aes(x = `1`, y = `2`, col = time)) +
-  geom_point(size = 3) + coord_fixed()
-```
-
diff -r 157dc02992d9 -r 405d8fa2f560 DESeq_results.xml
--- a/DESeq_results.xml	Tue Feb 27 20:44:34 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-<tool id="deseq_results" name="DESeq2: Results" version="2.0.1">
-    <requirements>
-        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
-        <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="1.6">r-rmarkdown</requirement>
-        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
-        <requirement type="package" version="0.2">r-dt</requirement>
-        <requirement type="package" version="1.0.8">r-pheatmap</requirement>
-    </requirements>
-    <description>
-        An R Markdown tool to display DESeq analysis.
-    </description>
-    <stdio>
-        <!--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_results_render.R'
-
-            -e $echo
-		    -o $report
-		    -d $report.files_path
-		    -s $sink_message
-		    -t '${__tool_directory__}'
-
-            ## 1. input data
-
-            -W $deseq_workspace
-            -C '$contrast_factor'
-            -T '$treatment'
-            -K '$condition'
-
-            -M '$clustering_factors'
-
-            ## 2. output report and report site directory
-            -R $deseq_results
-
-
-        ]]>
-    </command>
-    <inputs>
-        <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 format="html" name="report" label="DESeq results report on ${on_string}" />
-        <data format="txt" name="sink_message" label="Warnings and Errors" 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 type="bibtex">
-            @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>
-        <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},
-            journal={R package version 0.9},
-            volume={6},
-            year={2016}
-            }
-        </citation>
-        <citation type="bibtex">
-            @book{xie2015dynamic,
-            title={Dynamic Documents with R and knitr},
-            author={Xie, Yihui},
-            volume={29},
-            year={2015},
-            publisher={CRC Press}
-            }
-        </citation>
-    </citations>
-</tool>
\ No newline at end of file
diff -r 157dc02992d9 -r 405d8fa2f560 DESeq_results_render.R
--- a/DESeq_results_render.R	Tue Feb 27 20:44:34 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-##============ Sink warnings and errors to a file ==============
-## use the sink() function to wrap all code within it.
-##==============================================================
-zz = file('warnings_and_errors.txt')
-sink(zz)
-sink(zz, type = 'message')
-
-#------------import libraries--------------------
-options(stringsAsFactors = FALSE)
-
-library(getopt)
-library(rmarkdown)
-library(DESeq2)
-library(pheatmap)
-library(DT)
-library(ggplot2)
-library(genefilter)
-library(RColorBrewer)
-#------------------------------------------------
-
-
-#------------get arguments into R--------------------
-# getopt_specification_matrix(extract_short_flags('DESeq_results.xml')) %>%
-#   write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
-
-
-spec_matrix = as.matrix(
-  data.frame(stringsAsFactors=FALSE,
-              long_flags = c("X_e", "X_W", "X_C", "X_T", "X_K", "X_M", "X_o",
-                             "X_d", "X_s", "X_R", "X_t"),
-             short_flags = c("e", "W", "C", "T", "K", "M", "o", "d", "s", "R",
-                             "t"),
-     argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
-         data_type_flags = c("character", "character", "character", "character",
-                             "character", "character", "character",
-                             "character", "character", "character", "character")
-  )
-)
-opt = getopt(spec_matrix)
-opt
-#----------------------------------------------------
-
-
-#-----------using passed arguments in R 
-#           to define system environment variables---
-do.call(Sys.setenv, opt[-1])
-#----------------------------------------------------
-
-#---------- often used variables ----------------
-# OUTPUT_DIR: path to the output associated directory, which stores all outputs
-# TOOL_DIR: path to the tool installation directory
-# RMD_NAME: name of Rmd file to be rendered
-# OUTPUT_REPORT: path to galaxy output report
-OUTPUT_DIR = opt$X_d
-TOOL_DIR =   opt$X_t
-RMD_NAME = 'DESeq_results.Rmd'
-OUTPUT_REPORT = opt$X_o
-
-# create the output associated directory to store all outputs
-dir.create(OUTPUT_DIR, recursive = TRUE)
-
-#-----------------render Rmd--------------
-render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
-#------------------------------------------
-
-#==============the end==============
-
-
-##--------end of code rendering .Rmd templates----------------
-sink()
-##=========== End of sinking output=============================
\ No newline at end of file
diff -r 157dc02992d9 -r 405d8fa2f560 deseq2.Rmd
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq2.Rmd	Thu Mar 08 20:13:30 2018 -0500
@@ -0,0 +1,29 @@
+---
+title: 'HTML report title'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = as.logical(), 
+  error = TRUE
+)
+```
+
+
+# Code for computational analysis
+
+```{r 'step 1'}
+
+```
+
+```{r 'ste[ 2'}
+
+```
+
+
diff -r 157dc02992d9 -r 405d8fa2f560 deseq2.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq2.sh	Thu Mar 08 20:13:30 2018 -0500
@@ -0,0 +1,17 @@
+Rscript '${__tool_directory__}/deseq2_render.R'
+
+  -e $echo
+  -o $report
+  -d $report.files_path
+  -s $sink_message
+  -t '${__tool_directory__}' 
+  
+  -A $count_data
+  -B $column_data
+  -C $design_formula
+  -D $treatment_name
+  -E $treated
+  -F $untreated
+  -G $test_type
+  -H $fit_type
+  -I $alpha
\ No newline at end of file
diff -r 157dc02992d9 -r 405d8fa2f560 deseq2.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq2.xml	Thu Mar 08 20:13:30 2018 -0500
@@ -0,0 +1,106 @@
+<tool id="aurora_deseq2" name="Aurora DESeq2" version="2.2.0">
+    <description>Differential analysis of count data with the DESeq2 package</description>
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+        <requirement type="package" version="4.5.6">r-plotly</requirement>
+        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
+    </requirements>
+    <stdio>
+        <regex match="XXX" source="stderr" level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
+    </stdio>
+    <command><![CDATA[Rscript '${__tool_directory__}/deseq2_render.R'
+
+  -e $echo
+  -o $report
+  -d $report.files_path
+  -s $sink_message
+  -t '${__tool_directory__}' 
+  
+  -A $count_data
+  -B $column_data
+  -C $design_formula
+  -D $treatment_name
+  -E $treated
+  -F $untreated
+  -G $test_type
+  -H $fit_type
+  -I $alpha]]></command>
+    <inputs>
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
+               label="Display analysis code in report?"/>
+        <param type="data" name="count_data" label="Count data"
+               help="an RData file that stores the count matrix data. The file is generated from the aurora_htseq tool."
+               optional="False" format="rdata"/>
+        <param type="data" name="column_data" label="Column data"
+               help="A table file that stores column data for DESeq2 analysis. The first columns are the column names from the count matrix data. The remaining columns are experimental treatments."
+               optional="False" format="csv"/>
+        <param type="text" name="design_formula" label="Design formula"
+               help="The design formula expresses the variables which will be used in modeling. The formula should be a tilde (~) followed by the variables with plus signs between them, e.g., ~ condition1 + condition2"
+               optional="False">
+            <sanitizer sanitize="true">
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="~"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param type="text" name="treatment_name" label="Treatment name"
+               help="one of the treatment column names from the column data." optional="False"/>
+        <param type="text" name="treated" label="Treated"
+               help="A level from the specified treatment column that will be used as the treated group in the DESeq2 analysis."
+               optional="False"/>
+        <param type="text" name="untreated" label="Untreated"
+               help="A level from the specified treatment column that will be used as the untreated group in the DESeq2 analysis."
+               optional="False"/>
+        <param type="select" name="test_type" label="Test type" optional="False">
+            <option value="Wald" selected="true">Wald</option>
+            <option value="LRT" selected="false">Likelihood Ratio Test (LRT)</option>
+        </param>
+        <param type="select" name="fit_type" label="Fitting of dispersions"
+               help="either &quot;parametric&quot;, &quot;local&quot;, or &quot;mean&quot; for the type of fitting of dispersions to the mean intensity"
+               optional="False">
+            <option value="parametric" selected="true">parametric</option>
+            <option value="local" selected="false">local</option>
+            <option value="mean" selected="false">mean</option>
+        </param>
+        <param type="float" name="alpha" label="Alpha"
+               help="the significance cutoff used for optimizing the independent filtering (by default 0.1). If the adjusted p-value cutoff (FDR) will be a value other than 0.1, alpha should be set to that value."
+               optional="False" value="0.1" min="0" max="1"/>
+    </inputs>
+    <outputs>
+        <data format="html" name="report" label="tool report"/>
+        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
+    </outputs>
+    <citations>
+        <citation type="bibtex"><![CDATA[
+            @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},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[@article{love2014differential,
+  title={Differential analysis of count data--the DESeq2 package},
+  author={Love, Michael and Anders, Simon and Huber, Wolfgang},
+  journal={Genome Biol},
+  volume={15},
+  pages={550},
+  year={2014}
+}]]></citation>
+    </citations>
+</tool>
diff -r 157dc02992d9 -r 405d8fa2f560 deseq2_render.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq2_render.R	Thu Mar 08 20:13:30 2018 -0500
@@ -0,0 +1,55 @@
+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file('warnings_and_errors.txt')
+sink(zz)
+sink(zz, type = 'message')
+
+#------------import libraries--------------------
+options(stringsAsFactors = FALSE)
+
+library(getopt)
+library(rmarkdown)
+library(ggplot2)
+library(plotly)
+library(htmltools)
+#------------------------------------------------
+
+
+#------------get arguments into R--------------------
+library(dplyr)
+getopt_specification_matrix(extract_short_flags('deseq2.xml')) %>%
+  write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
+
+
+spec_matrix = as.matrix()
+opt = getopt(spec_matrix)
+#----------------------------------------------------
+
+
+#-----------using passed arguments in R 
+#           to define system environment variables---
+do.call(Sys.setenv, opt[-1])
+#----------------------------------------------------
+
+#---------- often used variables ----------------
+# OUTPUT_DIR: path to the output associated directory, which stores all outputs
+# TOOL_DIR: path to the tool installation directory
+OUTPUT_DIR = ''
+TOOL_DIR =   ''
+RMD_NAME = ''
+OUTPUT_REPORT = opt$X_o
+
+# create the output associated directory to store all outputs
+dir.create(OUTPUT_DIR, recursive = TRUE)
+
+#-----------------render Rmd--------------
+render(paste0(TOOL_DIR, RMD_NAME, sep = '/'), output_file = OUTPUT_REPORT)
+#------------------------------------------
+
+#==============the end==============
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
\ No newline at end of file
diff -r 157dc02992d9 -r 405d8fa2f560 spec.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spec.txt	Thu Mar 08 20:13:30 2018 -0500
@@ -0,0 +1,6 @@
+long_flags,short_flags,argument_mask_flags,data_type_flags
+X_e,e,1,character
+X_o,o,1,character
+X_d,d,1,character
+X_s,s,1,character
+X_t,t,1,character