# HG changeset patch
# User mingchen0919
# Date 1519757729 18000
# Node ID 8b324ea5dc8afb185194ad7ccbce94df3b06f6bc
# Parent  6b12f3dc358aac48eef55edb7bc2ffd2e096f51d
2.0.1

diff -r 6b12f3dc358a -r 8b324ea5dc8a DESeq.xml
--- a/DESeq.xml	Tue Feb 27 13:04:12 2018 -0500
+++ b/DESeq.xml	Tue Feb 27 13:55:29 2018 -0500
@@ -1,4 +1,4 @@
-<tool name="Tool report" id='aurora_tool_report' version="1.0.0">
+<tool name="Tool report" id='aurora_tool_report' version="2.0.1">
     <description>
         "some description"
     </description>
@@ -6,6 +6,9 @@
         <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"
diff -r 6b12f3dc358a -r 8b324ea5dc8a DESeq_render.R
--- a/DESeq_render.R	Tue Feb 27 13:04:12 2018 -0500
+++ b/DESeq_render.R	Tue Feb 27 13:55:29 2018 -0500
@@ -10,12 +10,9 @@
 
 library(getopt)
 library(rmarkdown)
-library(htmltools)
 library(dplyr)
-library(stringi)
 library(DESeq2)
 library(pheatmap)
-library(RColorBrewer)
 library(DT)
 #------------------------------------------------
 
diff -r 6b12f3dc358a -r 8b324ea5dc8a DESeq_results.xml
--- a/DESeq_results.xml	Tue Feb 27 13:04:12 2018 -0500
+++ b/DESeq_results.xml	Tue Feb 27 13:55:29 2018 -0500
@@ -1,17 +1,10 @@
-<tool id="DESeq_results" name="DESeq2: Results" version="2.0.0">
+<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="1.2">r-rmarkdown</requirement>
-        <requirement type="package" version="1.8.4">r-plyr</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</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>
-        <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>
diff -r 6b12f3dc358a -r 8b324ea5dc8a DESeq_results_render.R
--- a/DESeq_results_render.R	Tue Feb 27 13:04:12 2018 -0500
+++ b/DESeq_results_render.R	Tue Feb 27 13:55:29 2018 -0500
@@ -4,10 +4,7 @@
 library(dplyr)
 library(DESeq2)
 library(pheatmap)
-library(genefilter)
 library(DT)
-library(stringi)
-library(RColorBrewer)
 library(ggplot2)
 
 ##============ Sink warnings and errors to a file ==============
diff -r 6b12f3dc358a -r 8b324ea5dc8a o-DESeq.xml
--- a/o-DESeq.xml	Tue Feb 27 13:04:12 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,120 +0,0 @@
-<tool id="DESeq" name="DESeq2: DESeq" version="2.0.0">
-    <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="1.8.4">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>
-        <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>
-        <!--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
-            ##----- 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
-		    -r $report
-		    -d $report.files_path
-		    -s $sink_message
-		    -w $deseq_workspace
-
-		    ## 3. Rmd templates from the tool directory
-            -t '${__tool_directory__}/DESeq.Rmd'
-
-
-
-        ]]>
-    </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 ${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 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 6b12f3dc358a -r 8b324ea5dc8a o-DESeq_render.R
--- a/o-DESeq_render.R	Tue Feb 27 13:04:12 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-library(getopt)
-library(rmarkdown)
-library(htmltools)
-library(dplyr)
-library(stringi)
-library(DESeq2)
-library(pheatmap)
-library(RColorBrewer)
-library(DT)
-
-##============ 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')
-  ##---------below is the code for rendering .Rmd templates-----
-  
-  ##=============STEP 1: handle command line arguments==========
-  ##
-  ##============================================================
-  # column 1: the long flag name
-  # column 2: the short flag alias. A SINGLE character string
-  # column 3: argument mask
-  #           0: no argument
-  #           1: argument required
-  #           2: argument is optional
-  # column 4: date type to which the flag's argument shall be cast.
-  #           possible values: logical, integer, double, complex, character.
-  #-------------------------------------------------------------
-  #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
-  # 1. short flag alias should match the flag in the command section in the XML file.
-  # 2. long flag name can be any legal R variable names
-  # 3. two names in args_list can have common string but one name should not be a part of another name.
-  #    for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
-  #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-  args_list=list()
-  ##------- 1. input data ---------------------
-  args_list$ECHO = c('echo', 'e', '1', 'character')
-  args_list$COUNT_FILE_PATHS = c('count_file_paths', 'P', '1', 'character')
-  args_list$COUNT_FILE_NAMES = c('count_file_names', 'N', '1', 'character')
-  args_list$SAMPLE_TABLE = c('sample_table', 'S', '1', 'character')
-  args_list$DESIGN_FORMULA = c('design_formula', 'p', '1', 'character')
-  ##--------2. output report and outputs --------------
-  args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
-  args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
-  args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
-  args_list$WORKSPACE = c('deseq_workspace', 'w', '1', 'character')
-  ##--------3. .Rmd templates in the tool directory ----------
-  args_list$deseq_RMD = c('deseq_rmd', 't', '1', 'character')
-  ##-----------------------------------------------------------
-  opt = getopt(t(as.data.frame(args_list)))
-
-
-  
-  ##=======STEP 2: create report directory (optional)==========
-  ##
-  ##===========================================================
-  dir.create(opt$report_dir)
-  
-  ##=STEP 3: replace placeholders in .Rmd with argument values=
-  ##
-  ##===========================================================
-  #++ need to replace placeholders with args values one by one+
-  readLines(opt$deseq_rmd) %>%
-    (function(x) {
-      gsub('ECHO', opt$echo, x)
-    }) %>%
-    (function(x) {
-      gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
-    }) %>%
-    (function(x) {
-      gsub('DESIGN_FORMULA', opt$design_formula, x)
-    }) %>%
-    (function(x) {
-      gsub('REPORT_DIR', opt$report_dir, x)
-    }) %>%
-    (function(x) {
-      fileConn = file('deseq.Rmd')
-      writeLines(x, con=fileConn)
-      close(fileConn)
-    })
-  
-
-  ##=============STEP 4: render .Rmd templates=================
-  ##
-  ##===========================================================
-  render('deseq.Rmd', output_file = opt$report_html)
-
-
-  ##--------end of code rendering .Rmd templates----------------
-sink()
-##=========== End of sinking output=============================
\ No newline at end of file