# HG changeset patch
# User lgueguen
# Date 1469180353 14400
# Node ID 581d217c7337009b078c793fc5b52acb87b5b0e9
Planemo upload
diff -r 000000000000 -r 581d217c7337 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,53 @@
+-----------------------------------------------------------
+SARTools-Galaxy: a galaxy wrapper for SARTools version 1.2.0
+-----------------------------------------------------------
+
+[![Build Status](https://travis-ci.org/PF2-pasteur-fr/SARTools-Galaxy.svg?branch=master)](https://travis-ci.org/PF2-pasteur-fr/SARTools-Galaxy)
+
+Description:
+------------
+ SARTools is a R package dedicated to the differential analysis of RNA-seq data.
+
+ SARTools provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis. Note that SARTools does not intend to replace DESeq2 or edgeR: it simply provides an environment to go with them. For more details about the methodology behind DESeq2 or edgeR, the user should read their documentations and papers.
+
+Requirements:
+-------------
+ R (3.2.2 or higher), Bio-conductor package
+ SARTools package (1.2.0)
+ other R packages: DESeq2 (1.10.0 or higher), edgeR (3.12.0 or higher), genefilter, xtable and knitr
+ Rscript
+
+ SARTools 1.2.0 can be downloaded on github (https://github.com/PF2-pasteur-fr/SARTools). More information about installation can be found at this url.
+
+Requirements using Conda:
+-------------------------
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/r-sartools/README.html)
+
+[Conda](http://conda.pydata.org/) is package manager that among many other things can be used to manage Python packages.
+
+
+```
+#To install miniconda2
+#http://conda.pydata.org/miniconda.html
+#To install the SARTools R library using conda:
+conda install r-sartools
+#To set an environment:
+conda create -n r-sartools r-sartools`
+#To activate the environment:
+. activate r-sartools
+```
+
+
+Test:
+-----
+
+`planemo test` using conda: passed
+
+
+References:
+-----------
+ The SARTools package has been developped at PF2 - Institut Pasteur by M.-A. Dillies and H. Varet (hugo.varet@pasteur.fr).
+ Thanks to cite H. Varet, L. Brillet-Guéguen, J.-Y. Coppee and M.-A. Dillies, SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One, 2016, doi: http://dx.doi.org/10.1371/journal.pone.0157022 when using this tool for any analysis published.
+
+ The Galaxy wrapper and scripts have been developped by Loraine Brillet-Guéguen, Institut Français de Bioinformatique
+
diff -r 000000000000 -r 581d217c7337 abims_sartools_deseq2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_sartools_deseq2.xml Fri Jul 22 05:39:13 2016 -0400
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+
+
+
+ Compare two or more biological conditions in a RNA-Seq framework with DESeq2
+
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+ macros.xml
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+ @ARTICLE{Cook77,
+ author = {R.-D. Cook},
+ title = {Detection of Influential Observation in Linear Regression},
+ journal = {Technometrics},
+ year = {1977},
+ month = {February}
+ }
+ @ARTICLE{Bourgon10,
+ author = {R. Bourgon, R. Gentleman, and W. Huber},
+ title = {Independent filtering increases detection power for high-throughput experiments},
+ journal = {PNAS},
+ year = {2010},
+ volume = {107},
+ number = {21},
+ pages = {9546–9551},
+ note = {URL: http://www.pnas.org/content/107/21/9546.long}
+ }
+
+
+
diff -r 000000000000 -r 581d217c7337 abims_sartools_deseq2_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_sartools_deseq2_wrapper.py Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,127 @@
+#abims_sartools_deseq2_wrapper.py
+#Author: Loraine Gueguen
+# imports
+import os, argparse
+
+
+
+def main():
+
+ print("Start of galaxy wrapper")
+
+ #Check R and Rscript are installed
+ check_r_cmd="command -v R >/dev/null 2>&1 || { echo >&2 'This tool requires R but it is not installed. Aborting.'; exit 1; }"
+ check_rscript_cmd="command -v Rscript >/dev/null 2>&1 || { echo >&2 'This tool requires Rscript but it is not installed. Aborting.'; exit 1; }"
+ os.system(check_r_cmd)
+ os.system(check_rscript_cmd)
+
+ #Get arguments
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--projectName')
+ parser.add_argument('--author')
+ parser.add_argument('--targetFile')
+ parser.add_argument('--rawDir')
+ parser.add_argument('--featuresToRemove')
+ parser.add_argument('--varInt')
+ parser.add_argument('--condRef')
+ parser.add_argument('--batch')
+ parser.add_argument('--fitType')
+ parser.add_argument('--cooksCutoff')
+ parser.add_argument('--independentFiltering')
+ parser.add_argument('--alpha')
+ parser.add_argument('--pAdjustMethod')
+ parser.add_argument('--typeTrans')
+ parser.add_argument('--locfunc')
+ parser.add_argument('--colors')
+ parser.add_argument('--figures_html')
+ parser.add_argument('--figures_html_files_path')
+ parser.add_argument('--tables_html')
+ parser.add_argument('--tables_html_files_path')
+ parser.add_argument('--rdata')
+ parser.add_argument('--report_html')
+ parser.add_argument('--log')
+ args = parser.parse_args()
+ projectName=args.projectName
+ author=args.author
+ targetFile=args.targetFile
+ rawDir=args.rawDir
+ featuresToRemove=args.featuresToRemove
+ varInt=args.varInt
+ condRef=args.condRef
+ batch=args.batch
+ fitType=args.fitType
+ cooksCutoff=args.cooksCutoff
+ independentFiltering=args.independentFiltering
+ alpha=args.alpha
+ pAdjustMethod=args.pAdjustMethod
+ typeTrans=args.typeTrans
+ locfunc=args.locfunc
+ colors=args.colors
+ figures_html=args.figures_html
+ figures_html_files_path=args.figures_html_files_path
+ tables_html=args.tables_html
+ tables_html_files_path=args.tables_html_files_path
+ rdata=args.rdata
+ report_html=args.report_html
+ log=args.log
+ #Print the parameters selected
+ print("Wrapper arguments: %s") %(args)
+
+ #Get the working directory path
+ working_directory = os.getcwd()
+ #Get the script directory path
+ script_directory=os.path.dirname(os.path.realpath(__file__))
+
+ #Unzip files from rawDir
+ rawDir_unzipped_path=working_directory+"/rawDir_unzipped"
+ os.mkdir(rawDir_unzipped_path)
+ unzip_cmd="unzip -j %s -d %s" % (rawDir,rawDir_unzipped_path) #-j arg: junk paths
+ os.system(unzip_cmd)
+
+ #Create the command
+ cmd="Rscript --no-save --no-restore %s/template_script_DESeq2_CL.r --projectName %s --author %s " % (script_directory,projectName,author)
+ cmd+="--targetFile %s --rawDir %s --featuresToRemove %s --varInt %s --condRef %s " % (targetFile,rawDir_unzipped_path,featuresToRemove,varInt,condRef)
+ if batch and batch!="NULL":
+ cmd+="--batch %s " % (batch)
+ if fitType:
+ cmd+="--fitType %s " % (fitType)
+ if cooksCutoff:
+ cmd+="--cooksCutoff %s " % (cooksCutoff)
+ if independentFiltering:
+ cmd+="--independentFiltering %s " % (independentFiltering)
+ if alpha:
+ cmd+="--alpha %s " % (alpha)
+ if pAdjustMethod:
+ cmd+="--pAdjustMethod %s " % (pAdjustMethod)
+ if typeTrans:
+ cmd+="--typeTrans %s " % (typeTrans)
+ if locfunc:
+ cmd+="--locfunc %s " % (locfunc)
+ if colors:
+ cmd+="--colors %s " % (colors)
+ cmd+="> %s 2>&1" % (log)
+ print("Rscript command: %s") % (cmd)
+ os.system(cmd)
+
+ #Get output files
+ os.mkdir(figures_html_files_path)
+ os.mkdir(tables_html_files_path)
+ rsync_figures_dir_cmd="rsync -r figures/* %s/." % (figures_html_files_path)
+ rsync_tables_dir_cmd="rsync -r tables/* %s/." % (tables_html_files_path)
+ os.system(rsync_figures_dir_cmd)
+ os.system(rsync_tables_dir_cmd)
+ figures_html_create_cmd="python %s/make_html.py --tool SARTools_DESeq2 --output_type Figures --output_dir %s --output_html %s" % (script_directory,figures_html_files_path,figures_html)
+ tables_html_create_cmd="python %s/make_html.py --tool SARTools_DESeq2 --output_type Tables --output_dir %s --output_html %s" % (script_directory,tables_html_files_path,tables_html)
+ os.system(figures_html_create_cmd)
+ os.system(tables_html_create_cmd)
+ rsync_rdata_file_cmd="rsync %s.RData %s" % (projectName,rdata)
+ rsync_report_file_cmd="rsync %s_report.html %s" % (projectName,report_html)
+ os.system(rsync_rdata_file_cmd)
+ os.system(rsync_report_file_cmd)
+
+ print("End of galaxy wrapper")
+
+if __name__ == '__main__':
+ main()
+
+
diff -r 000000000000 -r 581d217c7337 abims_sartools_edger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_sartools_edger.xml Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,190 @@
+
+
+
+ Compare two or more biological conditions in a RNA-Seq framework with edgeR
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+ macros.xml
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+ Hide
+ Show
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diff -r 000000000000 -r 581d217c7337 abims_sartools_edger_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_sartools_edger_wrapper.py Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,119 @@
+#abims_sartools_edger_wrapper.py
+#Author: Loraine Gueguen
+# imports
+import os, argparse
+
+
+
+def main():
+
+ print("Start of galaxy wrapper")
+
+ #Check R and Rscript are installed
+ check_r_cmd="command -v R >/dev/null 2>&1 || { echo >&2 'This tool requires R but it is not installed. Aborting.'; exit 1; }"
+ check_rscript_cmd="command -v Rscript >/dev/null 2>&1 || { echo >&2 'This tool requires Rscript but it is not installed. Aborting.'; exit 1; }"
+ os.system(check_r_cmd)
+ os.system(check_rscript_cmd)
+
+ #Get arguments
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--projectName')
+ parser.add_argument('--author')
+ parser.add_argument('--targetFile')
+ parser.add_argument('--rawDir')
+ parser.add_argument('--featuresToRemove')
+ parser.add_argument('--varInt')
+ parser.add_argument('--condRef')
+ parser.add_argument('--batch')
+ parser.add_argument('--alpha')
+ parser.add_argument('--pAdjustMethod')
+ parser.add_argument('--cpmCutoff')
+ parser.add_argument('--geneSelection')
+ parser.add_argument('--normalizationMethod')
+ parser.add_argument('--colors')
+ parser.add_argument('--figures_html')
+ parser.add_argument('--figures_html_files_path')
+ parser.add_argument('--tables_html')
+ parser.add_argument('--tables_html_files_path')
+ parser.add_argument('--rdata')
+ parser.add_argument('--report_html')
+ parser.add_argument('--log')
+ args = parser.parse_args()
+ projectName=args.projectName
+ author=args.author
+ targetFile=args.targetFile
+ rawDir=args.rawDir
+ featuresToRemove=args.featuresToRemove
+ varInt=args.varInt
+ condRef=args.condRef
+ batch=args.batch
+ alpha=args.alpha
+ pAdjustMethod=args.pAdjustMethod
+ cpmCutoff=args.cpmCutoff
+ geneSelection=args.geneSelection
+ normalizationMethod=args.normalizationMethod
+ colors=args.colors
+ figures_html=args.figures_html
+ figures_html_files_path=args.figures_html_files_path
+ tables_html=args.tables_html
+ tables_html_files_path=args.tables_html_files_path
+ rdata=args.rdata
+ report_html=args.report_html
+ log=args.log
+ #Print the parameters selected
+ print("Wrapper arguments: %s") %(args)
+
+ #Get the working directory path
+ working_directory = os.getcwd()
+ #Get the script directory path
+ script_directory=os.path.dirname(os.path.realpath(__file__))
+
+ #Unzip files from rawDir
+ rawDir_unzipped_path=working_directory+"/rawDir_unzipped"
+ os.mkdir(rawDir_unzipped_path)
+ unzip_cmd="unzip -j %s -d %s" % (rawDir,rawDir_unzipped_path) #-j arg: junk paths
+ os.system(unzip_cmd)
+
+ #Create the command
+ cmd="Rscript --no-save --no-restore %s/template_script_edgeR_CL.r --projectName %s --author %s " % (script_directory,projectName,author)
+ cmd+="--targetFile %s --rawDir %s --featuresToRemove %s --varInt %s --condRef %s " % (targetFile,rawDir_unzipped_path,featuresToRemove,varInt,condRef)
+ if batch and batch!="NULL":
+ cmd+="--batch %s " % (batch)
+ if alpha:
+ cmd+="--alpha %s " % (alpha)
+ if pAdjustMethod:
+ cmd+="--pAdjustMethod %s " % (pAdjustMethod)
+ if cpmCutoff:
+ cmd+="--cpmCutoff %s " % (cpmCutoff)
+ if geneSelection:
+ cmd+="--gene.selection %s " % (geneSelection)
+ if normalizationMethod:
+ cmd+="--normalizationMethod %s " % (normalizationMethod)
+ if colors:
+ cmd+="--colors %s " % (colors)
+ cmd+="> %s 2>&1" % (log)
+ print("Rscript command: %s") % (cmd)
+ os.system(cmd)
+
+ #Get output files
+ os.mkdir(figures_html_files_path)
+ os.mkdir(tables_html_files_path)
+ rsync_figures_dir_cmd="rsync -r figures/* %s/." % (figures_html_files_path)
+ rsync_tables_dir_cmd="rsync -r tables/* %s/." % (tables_html_files_path)
+ os.system(rsync_figures_dir_cmd)
+ os.system(rsync_tables_dir_cmd)
+ figures_html_create_cmd="python %s/make_html.py --tool SARTools_edgeR --output_type Figures --output_dir %s --output_html %s" % (script_directory,figures_html_files_path,figures_html)
+ tables_html_create_cmd="python %s/make_html.py --tool SARTools_edgeR --output_type Tables --output_dir %s --output_html %s" % (script_directory,tables_html_files_path,tables_html)
+ os.system(figures_html_create_cmd)
+ os.system(tables_html_create_cmd)
+ rsync_rdata_file_cmd="rsync %s.RData %s" % (projectName,rdata)
+ rsync_report_file_cmd="rsync %s_report.html %s" % (projectName,report_html)
+ os.system(rsync_rdata_file_cmd)
+ os.system(rsync_report_file_cmd)
+
+ print("End of galaxy wrapper")
+
+if __name__ == '__main__':
+ main()
+
+
diff -r 000000000000 -r 581d217c7337 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,261 @@
+
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+
+ r-sartools
+ r-optparse
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+ --projectName $projectName
+ --author $author
+ --targetFile $targetFile
+ --rawDir $rawDir
+ --featuresToRemove $featuresToRemove
+ --varInt $varInt
+ --condRef $condRef
+
+
+
+ #if $advanced_parameters.batch_condition.condition:
+ --batch $advanced_parameters.batch_condition.batch
+ #else:
+ --batch NULL
+ #end if
+
+
+
+ --figures_html $figures_html
+ --figures_html_files_path $figures_html.files_path
+ --tables_html $tables_html
+ --tables_html_files_path $tables_html.files_path
+ --rdata $rdata
+ --report_html $report_html
+ --log $log
+
+
+
+
+ \S+
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+ \S+
+
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+ \S+
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+ BY
+ bonferroni
+ fdr
+ hochberg
+ holm
+ hommel
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+ \S+
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+
+
+
+.. class:: infomark
+
+**Authors** M.-A. Dillies and H. Varet
+
+ | If you use this tool, please cite: H. Varet, L. Brillet-Guéguen, J.-Y. Coppee and M.-A. Dillies, SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One, 2016, doi: http://dx.doi.org/10.1371/journal.pone.0157022
+ | For details about this tool, please go to https://github.com/PF2-pasteur-fr/SARTools
+
+.. class:: infomark
+
+**Galaxy integration** Loraine Brillet-Guéguen, Institut Français de Bioinformatique
+
+ | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
+
+---------------------------------------------------
+
+
+
+ | SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis.
+ | Note that SARTools does not intend to replace DESeq2 or edgeR: it simply provides an environment to go with them. For more details about the methodology behind DESeq2 or edgeR, the user should read their documentations and papers.
+
+
+
+.. class:: warningmark
+
+If the counts and the target files are not supplied in the required formats, the workflow will probably crash and will not be able to run the analysis.
+
+
++---------------------------+-----------+
+| Parameter : num + label | Format |
++===========================+===========+
+| 1 : Design / target file | tabular |
++---------------------------+-----------+
+| 2 : Raw counts files | zip |
++---------------------------+-----------+
+
+
+Design/target file:
+ | The user has to supply a tab delimited file which describes the experiment, i.e. which contains the name of the biological condition associated with each sample. This file is called ”target” as a reference to the target file needed when using the limma package [1]. This file has one row per sample and is composed of at least three columns with headers:
+
+ * column 1 : unique names of the samples (short but informative as they will be displayed on all the figures);
+ * column 2 : name of the count files;
+ * column 3 : biological conditions;
+ * optional columns : further information about the samples (day of library preparation for example).
+
+
+- Example of a target file::
+
+ label files group
+ s1c1 count_file_sample1_cond1.txt cond1
+ s2c1 count_file_sample2_cond1.txt cond1
+ s1c2 count_file_sample1_cond2.txt cond2
+ s2c2 count_file_sample2_cond2.txt cond2
+
+
+Zip file containing raw counts files:
+ | The statistical analysis assumes that reads have already been mapped and that counts per feature (gene or transcript) are available. If counting has been done with HTSeq-count [2, 3], output files are ready to be loaded in R with the dedicated SARTools function. If not, the user must supply, in a zip file, one count file per sample with two tab delimited columns without header:
+
+ * column 1 : the unique IDs of the features;
+ * column 2 : the raw counts associated with these features (null or positive integers).
+
+
+
+ * **projectName:** name of the project;
+ * **author:** author of the analysis;
+ * **featuresToRemove:** character vector containing the IDs of the features to remove before running the analysis (default are "alignment not unique", "ambiguous", "no feature", "not aligned", "too low aQual" to remove HTSeq-count specific rows);
+ * **varInt:** variable of interest, i.e. biological condition, in the target file ("group" by default);
+ * **condRef:** reference biological condition used to compute fold-changes (no default, must be one of the levels of varInt);
+
+
+
+**Report:**
+
+
+ | Give details about the methodology, the different steps and the results. It displays all the figures produced and the most important results of the differential analysis as the number of up- and down-regulated features.
+ | The user should read the full HTML report and closely analyze each figure to check that the analysis ran smoothly.
+
+
+**Tables:**
+
+
+ * **TestVsRef.complete.txt:** contains all the features studied;
+ * **TestVsRef.down.txt:** contains only significant down-regulated features, i.e. less expressed in Test than in Ref;
+ * **TestVsRef.up.txt:** contains only significant up-regulated features i.e. more expressed in Test than in Ref.
+
+
+**Figures:**
+
+
+ * **MAplot.png:** MA-plot for each comparison (log ratio of the means vs intensity).
+ * **PCA.png:** first and second factorial planes of the PCA on the samples based on VST or rlog data;
+ * **barplotNull.png:** percentage of null counts per sample;
+ * **barplotTC.png:** total number of reads per sample;
+ * **cluster.png:** hierachical clustering of the samples (based on VST or rlog data);
+ * **countsBoxplot.png:** boxplots on raw and normalized counts;
+ * **densplot.png:** estimation of the density of the counts for each sample;
+ * **diagSizeFactorsHist.png:** diagnostic of the estimation of the size factors;
+ * **diagSizeFactorsTC.png:** plot of the size factors vs the total number of reads;
+ * **dispersionsPlot.png:** graph of the estimations of the dispersions and diagnostic of log-linearity of the dispersions;
+ * **majSeq.png:** percentage of reads caught by the feature having the highest count in each sample;
+ * **pairwiseScatter.png:** pairwise scatter plot between each pair of samples and SERE values;
+ * **rawpHist.png:** histogram of the raw p-values for each comparison;
+ * **volcanoPlot.png:** vulcano plot for each comparison (− log10 (adjusted P value) vs log ratio of the means).
+
+
+**R log file:**
+
+
+ | Give the R console outputs.
+
+
+**R objects (.RData file):**
+
+
+ | Give all the R objects created during the analysis is saved: it may be used to perform downstream analyses.
+
+
+
+ 10.1371/journal.pone.0157022
+ @INBOOK{Smyth05,
+ author = {G.-K. Smyth},
+ editor = {R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber},
+ chapter = {Limma: linear models for microarray data},
+ title = {Bioinformatics and Computational Biology Solutions Using R and Bioconductor},
+ publisher = {Springer},
+ year = {2005},
+ pages = {397–420}
+ }
+ 10.1093/bioinformatics/btu638
+ @ARTICLE{Benjamini95,
+ author = {Y. Benjamini and Y. Hochberg},
+ title = {Controlling the false discovery rate: a practical and powerful approach to multiple testing},
+ journal = {Journal of the Royal Statistical Society B},
+ year = {1995},
+ volume = {57},
+ pages = {289–300}
+ }
+ @ARTICLE{Benjamini01,
+ author = {Y. Benjamini and D. Yekutieli},
+ title = {The control of the false discovery rate in multiple testing under dependency},
+ journal = {Ann. Statist.},
+ year = {2001},
+ volume = {29},
+ number = {4},
+ pages = {1165–1188}
+ }
+
+
+
diff -r 000000000000 -r 581d217c7337 make_html.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_html.py Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,73 @@
+#Author: Loraine Gueguen
+
+import sys
+import os
+import time
+import argparse
+
+def getfSize(fpath,outpath):
+ """
+ format a nice file size string
+ """
+ size = ''
+ fp = os.path.join(outpath,fpath)
+ if os.path.isfile(fp):
+ size = '0 B'
+ n = float(os.path.getsize(fp))
+ if n > 2**20:
+ size = '%1.1f MB' % (n/2**20)
+ elif n > 2**10:
+ size = '%1.1f KB' % (n/2**10)
+ elif n > 0:
+ size = '%d B' % (int(n))
+ return size
+
+# Define option
+parser = argparse.ArgumentParser(description='Create an html page for downloading files from a directory')
+parser.add_argument('--tool', help='Galaxy tool', required=True)
+parser.add_argument('--output_type', help='figures or tables', required=True)
+parser.add_argument('--output_dir', help='Output directory', required=True)
+parser.add_argument('--output_html', help='Output HTML file name', default='', required=True)
+
+#Parse the command line
+args = parser.parse_args()
+tool=args.tool
+output_type=args.output_type
+output_dir=args.output_dir
+output_html=args.output_html
+
+
+debut_html="""
+
+
+
+
+
+
+ Galaxy Tool %s
+""" %(tool)
+
+fin_html=""
+
+html=debut_html
+run_date=time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+html+='Run at %s
\n'%run_date
+html+='%s available for downloading
\n'%output_type
+
+
+flist = os.listdir(output_dir)
+flist.sort()
+
+
+html+='Output File Name (click to view) Size \n'
+
+for f in flist :
+ size=getfSize(f,output_dir)
+ html+='%s %s \n'%(f,f,size)
+html+='
\n'
+
+html+=fin_html
+
+htmlf = file(output_html,'w')
+htmlf.write(html)
+htmlf.close()
diff -r 000000000000 -r 581d217c7337 pre_sartools.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pre_sartools.py Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,74 @@
+#!/usr/bin/env python
+#Author: Coline Billerey
+
+from os.path import basename, join
+from os import getcwd, system
+import argparse
+from shutil import copyfile
+import tempfile
+import csv
+
+def __main__():
+
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--batch')
+ parser.add_argument('--inputs', action='append' ,nargs='*')
+ parser.add_argument('--outfile')
+ parser.add_argument('--outarch')
+ args = parser.parse_args()
+
+ batch=args.batch
+ outfile=args.outfile
+ outarch=args.outarch
+ inputs=args.inputs
+ counts_files = open( outfile, 'w' )
+
+ working_directory = getcwd()
+ file_zip=working_directory+"/counts.zip"
+
+
+ zip_cmd='zip -j %s' % (file_zip)
+ if batch and batch!="NULL":
+ counts_files.write("label\tfiles\tgroup\tbatch\n")
+ for (level, filename, label, batch_name ) in inputs:
+ filename_base = basename(filename)
+ # For RSEM files we process files as HTSeq count output
+ tmpdir = tempfile.mkdtemp()
+ with open(filename, 'rb') as csvfile:
+ with open(join(tmpdir, basename(filename)), 'wb') as out:
+ spamwriter = csv.writer(out, delimiter='\t')
+ reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True)
+ if len(reader.fieldnames) > 2:
+ for row in reader:
+ spamwriter.writerow((row['gene_id'], int(float(row['effective_length']))))
+ zip_cmd += ' %s ' % (join(tmpdir, basename(filename)))
+ else :
+ zip_cmd += ' %s ' % (filename)
+ counts_files.write( label + "\t" + filename_base + "\t" + level + "\t" + batch_name + "\n" )
+ else :
+ counts_files.write("label\tfiles\tgroup\n")
+ for (level, filename, label) in inputs:
+ filename_base = basename(filename)
+ # For RSEM files we process files as HTSeq count output
+ tmpdir = tempfile.mkdtemp()
+ with open(filename, 'rb') as csvfile:
+ with open(join(tmpdir, basename(filename)), 'wb') as out:
+ spamwriter = csv.writer(out, delimiter='\t')
+ reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True)
+ if len(reader.fieldnames) > 2:
+ for row in reader:
+ spamwriter.writerow((row['gene_id'], int(float(row['effective_length']))))
+ zip_cmd += ' %s ' % (join(tmpdir, basename(filename)))
+ else:
+ zip_cmd += ' %s ' % (filename)
+
+ counts_files.write( label + "\t" + filename_base + "\t" + level + "\n" )
+
+ counts_files.close()
+ system(zip_cmd)
+ copyfile(file_zip,outarch)
+
+
+
+if __name__=="__main__":
+ __main__()
diff -r 000000000000 -r 581d217c7337 pre_sartools.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pre_sartools.xml Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,115 @@
+
+ generate design/target file and archive for SARTools inputs
+
+ pre_sartools.py
+ --outfile=$outfile
+ --outarch=$outarch
+ #if $batch_condition.condition:
+ --batch $batch_condition.condition
+ #for $i, $input in enumerate ( $batch_condition.levels ):
+ #for $j, $input_rep in enumerate ($input.rep_counts ):
+ --inputs "${input.level_name}" "${input_rep.count_data}" "${input_rep.label}" "${input_rep.batch_value}"
+ #end for
+ #end for
+ #else:
+ --batch NULL
+ #for $i, $input in enumerate ( $batch_condition.levels ):
+ #for $j, $input_rep in enumerate ($input.rep_counts ):
+ --inputs "${input.level_name}" "${input_rep.count_data}" "${input_rep.label}"
+ #end for
+ #end for
+ #end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+-----------
+Description
+-----------
+ * This tool creates a target file and an archive to use in input of SARTools.
+ * For details about SARTools, please visit https://github.com/PF2-pasteur-fr/SARTools.
+ * The count file must be outcoming from htseq-count or RSEM
+
+ * In input of SARTools, don't change the "factor of interest", by default is group but you need to change the "Reference biological condition" in order to correspond to one name of the groups.
+ * If you add a blocking factor, you need to specify it in "Advanced Parameters" of SARTools
+
+
diff -r 000000000000 -r 581d217c7337 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,4 @@
+
+
+
+
diff -r 000000000000 -r 581d217c7337 template_script_DESeq2_CL.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/template_script_DESeq2_CL.r Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,192 @@
+#!/local/gensoft2/exe/R/3.1.2/bin/Rscript
+
+# to run this script, use one of these commands:
+# Rscript --no-save --no-restore --verbose template_script_DESeq2_CL.r -r raw -v group -c T0 > log.txt 2>&1
+# Rscript template_script_DESeq2_CL.r -r raw -v group -c T0
+
+# to get help:
+# Rscript template_script_DESeq2_CL.r --help
+
+################################################################################
+### R script to compare several conditions with the SARTools and DESeq2 packages
+### Hugo Varet
+### April 20th, 2015
+### designed to be executed with SARTools 1.1.0
+################################################################################
+
+rm(list=ls()) # remove all the objects from the R session
+library(optparse) # to run the script in command lines
+
+# options list with associated default value.
+option_list <- list(
+make_option(c("-P", "--projectName"),
+ default=basename(getwd()),
+ dest="projectName",
+ help="name of the project used for the report [default: name of the current directory]."),
+
+make_option(c("-A", "--author"),
+ default=Sys.info()[7],
+ dest="author",
+ help="name of the report author [default: %default]."),
+
+make_option(c("-t", "--targetFile"),
+ default="target.txt",
+ dest="targetFile",
+ help="path to the design/target file [default: %default]."),
+
+make_option(c("-r", "--rawDir"),
+ default="raw",
+ dest="rawDir",
+ help="path to the directory containing the HTSeq files [default: %default]."),
+
+make_option(c("-F", "--featuresToRemove"),
+ default="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual",
+ dest="FTR",
+ help="names of the features to be removed, more than once can be specified [default: %default]"),
+
+make_option(c("-v", "--varInt"),
+ default="group",
+ dest="varInt",
+ help="factor of interest [default: %default]"),
+
+make_option(c("-c", "--condRef"),
+ default="WT",
+ dest="condRef",
+ help="reference biological condition [default: %default]"),
+
+make_option(c("-b", "--batch"),
+ default=NULL,
+ dest="batch",
+ help="blocking factor [default: %default] or \"batch\" for example"),
+
+make_option(c("-f", "--fitType"),
+ default="parametric",
+ dest="fitType",
+ help="mean-variance relationship: [default: %default] or local"),
+
+make_option(c("-o", "--cooksCutoff"),
+ default=TRUE,
+ dest="cooksCutoff",
+ help="perform the outliers detection (default is TRUE)"),
+
+make_option(c("-i", "--independentFiltering"),
+ default=TRUE,
+ dest="independentFiltering",
+ help="perform independent filtering (default is TRUE)"),
+
+make_option(c("-a", "--alpha"),
+ default=0.05,
+ dest="alpha",
+ help="threshold of statistical significance [default: %default]"),
+
+make_option(c("-p", "--pAdjustMethod"),
+ default="BH",
+ dest="pAdjustMethod",
+ help="p-value adjustment method: \"BH\" or \"BY\" [default: %default]"),
+
+make_option(c("-T", "--typeTrans"),
+ default="VST",
+ dest="typeTrans",
+ help="transformation for PCA/clustering: \"VST\" ou \"rlog\" [default: %default]"),
+
+make_option(c("-l", "--locfunc"),
+ default="median",
+ dest="locfunc",
+ help="median or shorth to estimate the size factors [default: %default]"),
+
+make_option(c("-C", "--colors"),
+ default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",
+ dest="cols",
+ help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]")
+)
+
+# now parse the command line to check which option is given and get associated values
+parser <- OptionParser(usage="usage: %prog [options]",
+ option_list=option_list,
+ description="Compare two or more biological conditions in a RNA-Seq framework with DESeq2.",
+ epilogue="For comments, bug reports etc... please contact Hugo Varet ")
+opt <- parse_args(parser, args=commandArgs(trailingOnly=TRUE), positional_arguments=0)$options
+
+# get options and arguments
+workDir <- getwd()
+projectName <- opt$projectName # name of the project
+author <- opt$author # author of the statistical analysis/report
+targetFile <- opt$targetFile # path to the design/target file
+rawDir <- opt$rawDir # path to the directory containing raw counts files
+featuresToRemove <- unlist(strsplit(opt$FTR, ",")) # names of the features to be removed (specific HTSeq-count information and rRNA for example)
+varInt <- opt$varInt # factor of interest
+condRef <- opt$condRef # reference biological condition
+batch <- opt$batch # blocking factor: NULL (default) or "batch" for example
+fitType <- opt$fitType # mean-variance relationship: "parametric" (default) or "local"
+cooksCutoff <- opt$cooksCutoff # outliers detection threshold (NULL to let DESeq2 choosing it)
+independentFiltering <- opt$independentFiltering # TRUE/FALSE to perform independent filtering (default is TRUE)
+alpha <- as.numeric(opt$alpha) # threshold of statistical significance
+pAdjustMethod <- opt$pAdjustMethod # p-value adjustment method: "BH" (default) or "BY"
+typeTrans <- opt$typeTrans # transformation for PCA/clustering: "VST" ou "rlog"
+locfunc <- opt$locfunc # "median" (default) or "shorth" to estimate the size factors
+colors <- unlist(strsplit(opt$cols, ",")) # vector of colors of each biologicial condition on the plots
+
+# print(paste("workDir", workDir))
+# print(paste("projectName", projectName))
+# print(paste("author", author))
+# print(paste("targetFile", targetFile))
+# print(paste("rawDir", rawDir))
+# print(paste("varInt", varInt))
+# print(paste("condRef", condRef))
+# print(paste("batch", batch))
+# print(paste("fitType", fitType))
+# print(paste("cooksCutoff", cooksCutoff))
+# print(paste("independentFiltering", independentFiltering))
+# print(paste("alpha", alpha))
+# print(paste("pAdjustMethod", pAdjustMethod))
+# print(paste("typeTrans", typeTrans))
+# print(paste("locfunc", locfunc))
+# print(paste("featuresToRemove", featuresToRemove))
+# print(paste("colors", colors))
+
+################################################################################
+### running script ###
+################################################################################
+# setwd(workDir)
+library(SARTools)
+
+# checking parameters
+problem <- checkParameters.DESeq2(projectName=projectName,author=author,targetFile=targetFile,
+ rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt,
+ condRef=condRef,batch=batch,fitType=fitType,cooksCutoff=cooksCutoff,
+ independentFiltering=independentFiltering,alpha=alpha,pAdjustMethod=pAdjustMethod,
+ typeTrans=typeTrans,locfunc=locfunc,colors=colors)
+if (problem) quit(save="yes")
+
+# loading target file
+target <- loadTargetFile(targetFile=targetFile, varInt=varInt, condRef=condRef, batch=batch)
+
+# loading counts
+counts <- loadCountData(target=target, rawDir=rawDir, featuresToRemove=featuresToRemove)
+
+# description plots
+majSequences <- descriptionPlots(counts=counts, group=target[,varInt], col=colors)
+
+# analysis with DESeq2
+out.DESeq2 <- run.DESeq2(counts=counts, target=target, varInt=varInt, batch=batch,
+ locfunc=locfunc, fitType=fitType, pAdjustMethod=pAdjustMethod,
+ cooksCutoff=cooksCutoff, independentFiltering=independentFiltering, alpha=alpha)
+
+# PCA + clustering
+exploreCounts(object=out.DESeq2$dds, group=target[,varInt], typeTrans=typeTrans, col=colors)
+
+# summary of the analysis (boxplots, dispersions, diag size factors, export table, nDiffTotal, histograms, MA plot)
+summaryResults <- summarizeResults.DESeq2(out.DESeq2, group=target[,varInt], col=colors,
+ independentFiltering=independentFiltering,
+ cooksCutoff=cooksCutoff, alpha=alpha)
+
+# save image of the R session
+save.image(file=paste0(projectName, ".RData"))
+
+# generating HTML report
+writeReport.DESeq2(target=target, counts=counts, out.DESeq2=out.DESeq2, summaryResults=summaryResults,
+ majSequences=majSequences, workDir=workDir, projectName=projectName, author=author,
+ targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt,
+ condRef=condRef, batch=batch, fitType=fitType, cooksCutoff=cooksCutoff,
+ independentFiltering=independentFiltering, alpha=alpha, pAdjustMethod=pAdjustMethod,
+ typeTrans=typeTrans, locfunc=locfunc, colors=colors)
diff -r 000000000000 -r 581d217c7337 template_script_edgeR_CL.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/template_script_edgeR_CL.r Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,175 @@
+#!/local/gensoft2/exe/R/3.1.2/bin/Rscript
+
+# to run this script, use one of these commands:
+# Rscript --no-save --no-restore --verbose template_script_edgeR_CL.r -r raw -v group -c T0 > log.txt 2>&1
+# Rscript template_script_edgeR_CL.r -r raw -v group -c T0
+
+# to get help:
+# Rscript template_script_edgeR_CL.r --help
+
+################################################################################
+### R script to compare several conditions with the SARTools and edgeR packages
+### Hugo Varet
+### April 20th, 2015
+### designed to be executed with SARTools 1.1.0
+################################################################################
+
+rm(list=ls()) # remove all the objects from the R session
+library(optparse) # to run the script in command lines
+
+# options list with associated default value.
+option_list <- list(
+make_option(c("-P", "--projectName"),
+ default=basename(getwd()),
+ dest="projectName",
+ help="name of the project used for the report [default: name of the current directory]."),
+
+make_option(c("-A", "--author"),
+ default=Sys.info()[7],
+ dest="author",
+ help="name of the report author [default: %default]."),
+
+make_option(c("-t", "--targetFile"),
+ default="target.txt",
+ dest="targetFile",
+ help="path to the design/target file [default: %default]."),
+
+make_option(c("-r", "--rawDir"),
+ default="raw",
+ dest="rawDir",
+ help="path to the directory containing the HTSeq files [default: %default]."),
+
+make_option(c("-F", "--featuresToRemove"),
+ default="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual",
+ dest="FTR",
+ help="names of the features to be removed, more than once can be specified [default: %default]"),
+
+make_option(c("-v", "--varInt"),
+ default="group",
+ dest="varInt",
+ help="factor of interest [default: %default]"),
+
+make_option(c("-c", "--condRef"),
+ default="WT",
+ dest="condRef",
+ help="reference biological condition [default: %default]"),
+
+make_option(c("-b", "--batch"),
+ default=NULL,
+ dest="batch",
+ help="blocking factor [default: %default] or \"batch\" for example"),
+
+make_option(c("-a", "--alpha"),
+ default=0.05,
+ dest="alpha",
+ help="threshold of statistical significance [default: %default]"),
+
+make_option(c("-p", "--pAdjustMethod"),
+ default="BH",
+ dest="pAdjustMethod",
+ help="p-value adjustment method: \"BH\" or \"BY\" [default: %default]"),
+
+make_option(c("-m", "--cpmCutoff"),
+ default=1,
+ dest="cpmCutoff",
+ help="counts-per-million cut-off to filter low counts"),
+
+make_option(c("-g", "--gene.selection"),
+ default="pairwise",
+ dest="gene.selection",
+ help="selection of the features in MDSPlot [default: %default]"),
+
+make_option(c("-n", "--normalizationMethod"),
+ default="TMM",
+ dest="normalizationMethod",
+ help="normalization method in calcNormFactors: \"TMM\", \"RLE\" or \"upperquartile\" [default: %default]"),
+
+make_option(c("-C", "--colors"),
+ default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",
+ dest="cols",
+ help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]")
+)
+
+# now parse the command line to check which option is given and get associated values
+parser <- OptionParser(usage="usage: %prog [options]",
+ option_list=option_list,
+ description="Compare two or more biological conditions in a RNA-Seq framework with edgeR.",
+ epilogue="For comments, bug reports etc... please contact Hugo Varet ")
+opt <- parse_args(parser, args=commandArgs(trailingOnly=TRUE), positional_arguments=0)$options
+
+# get options and arguments
+workDir <- getwd()
+projectName <- opt$projectName # name of the project
+author <- opt$author # author of the statistical analysis/report
+targetFile <- opt$targetFile # path to the design/target file
+rawDir <- opt$rawDir # path to the directory containing raw counts files
+featuresToRemove <- unlist(strsplit(opt$FTR, ",")) # names of the features to be removed (specific HTSeq-count information and rRNA for example)
+varInt <- opt$varInt # factor of interest
+condRef <- opt$condRef # reference biological condition
+batch <- opt$batch # blocking factor: NULL (default) or "batch" for example
+alpha <- as.numeric(opt$alpha) # threshold of statistical significance
+pAdjustMethod <- opt$pAdjustMethod # p-value adjustment method: "BH" (default) or "BY"
+gene.selection <- opt$gene.selection # selection of the features in MDSPlot
+normalizationMethod <- opt$normalizationMethod # normalization method in calcNormFactors
+cpmCutoff <- opt$cpmCutoff # counts-per-million cut-off to filter low counts
+colors <- unlist(strsplit(opt$cols, ",")) # vector of colors of each biologicial condition on the plots
+
+# print(paste("workDir", workDir))
+# print(paste("projectName", projectName))
+# print(paste("author", author))
+# print(paste("targetFile", targetFile))
+# print(paste("rawDir", rawDir))
+# print(paste("varInt", varInt))
+# print(paste("condRef", condRef))
+# print(paste("batch", batch))
+# print(paste("alpha", alpha))
+# print(paste("pAdjustMethod", pAdjustMethod))
+# print(paste("featuresToRemove", featuresToRemove))
+# print(paste("colors", colors))
+# print(paste("gene.selection", gene.selection))
+# print(paste("normalizationMethod", normalizationMethod))
+# print(paste("cpmCutoff", cpmCutoff))
+
+################################################################################
+### running script ###
+################################################################################
+# setwd(workDir)
+library(SARTools)
+
+# checking parameters
+problem <- checkParameters.edgeR(projectName=projectName,author=author,targetFile=targetFile,
+ rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt,
+ condRef=condRef,batch=batch,alpha=alpha,pAdjustMethod=pAdjustMethod,
+ cpmCutoff=cpmCutoff,gene.selection=gene.selection,
+ normalizationMethod=normalizationMethod,colors=colors)
+if (problem) quit(save="yes")
+
+# loading target file
+target <- loadTargetFile(targetFile=targetFile, varInt=varInt, condRef=condRef, batch=batch)
+
+# loading counts
+counts <- loadCountData(target=target, rawDir=rawDir, featuresToRemove=featuresToRemove)
+
+# description plots
+majSequences <- descriptionPlots(counts=counts, group=target[,varInt], col=colors)
+
+# edgeR analysis
+out.edgeR <- run.edgeR(counts=counts, target=target, varInt=varInt, condRef=condRef,
+ batch=batch, cpmCutoff=cpmCutoff, normalizationMethod=normalizationMethod,
+ pAdjustMethod=pAdjustMethod)
+
+# MDS + clustering
+exploreCounts(object=out.edgeR$dge, group=target[,varInt], gene.selection=gene.selection, col=colors)
+
+# summary of the analysis (boxplots, dispersions, export table, nDiffTotal, histograms, MA plot)
+summaryResults <- summarizeResults.edgeR(out.edgeR, group=target[,varInt], counts=counts, alpha=alpha, col=colors)
+
+# save image of the R session
+save.image(file=paste0(projectName, ".RData"))
+
+# generating HTML report
+writeReport.edgeR(target=target, counts=counts, out.edgeR=out.edgeR, summaryResults=summaryResults,
+ majSequences=majSequences, workDir=workDir, projectName=projectName, author=author,
+ targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt,
+ condRef=condRef, batch=batch, alpha=alpha, pAdjustMethod=pAdjustMethod, colors=colors,
+ gene.selection=gene.selection, normalizationMethod=normalizationMethod)
diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_KOvsWT.complete.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SARTools_DESeq2_KOvsWT.complete.txt Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,8218 @@
+Id WT1 WT2 KO1 KO2 norm.WT1 norm.WT2 norm.KO1 norm.KO2 baseMean WT KO FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks outlier
+feat0001 2728 1636 668 2378 1106 970 2553 2595 1806.13 1038 2574 2.451 1.293 5.37519651793256e-23 6.36948912861346e-22 0.0041 0.0086 0.0078 0.0078 TRUE NA NA
+feat0002 3169 1892 376 1228 1285 1121 1437 1340 1295.99 1203 1388 1.147 0.198 0.160735832870222 0.21103027167996 0.0056 0.0096 0.0088 0.0088 TRUE NA NA
+feat0003 2784 1626 622 2117 1129 964 2377 2311 1695.16 1046 2344 2.212 1.145 2.46807614980336e-17 2.02427530084789e-16 0.0062 0.0088 0.0083 0.0083 TRUE NA NA
+feat0004 6311 4283 374 1470 2560 2539 1429 1604 2032.99 2550 1516 0.602 -0.731 1.04715254885587e-08 4.04483408933959e-08 5e-04 0.0083 0.0072 0.0072 TRUE NA NA
+feat0005 12769 9132 718 3199 5179 5413 2744 3492 4206.76 5296 3118 0.596 -0.746 1.88312423678069e-08 7.1167767069692e-08 0.0144 0.0072 0.0083 0.0083 TRUE NA NA
+feat0006 3953 2867 666 2579 1603 1699 2545 2815 2165.68 1651 2680 1.619 0.695 3.02564035998192e-08 1.12082423279993e-07 0.0024 0.0082 0.0072 0.0072 TRUE NA NA
+feat0007 4070 2498 310 1039 1651 1481 1185 1134 1362.51 1566 1160 0.742 -0.431 0.0017821246875128 0.00345101690390565 0.0034 0.0094 0.0083 0.0083 TRUE NA NA
+feat0008 2750 2026 257 924 1115 1201 982 1009 1076.72 1158 996 0.863 -0.212 0.134629764575021 0.180478354843489 0 0.0103 0.0086 0.0086 TRUE NA NA
+feat0009 2044 1286 118 400 829 762 451 437 619.69 796 444 0.563 -0.829 7.71633809276032e-07 2.40922220777453e-06 0 0.0133 0.0113 0.0113 TRUE NA NA
+feat0010 3118 2361 511 1885 1265 1399 1953 2057 1668.57 1332 2005 1.501 0.586 7.73270297819381e-06 2.13511764456237e-05 0.003 0.0088 0.0077 0.0077 TRUE NA NA
+feat0011 9296 4990 501 1705 3770 2958 1915 1861 2625.87 3364 1888 0.565 -0.823 5.57421866989203e-09 2.22471048700155e-08 0.014 0.0078 0.0092 0.0092 TRUE NA NA
+feat0012 2933 2233 291 1158 1190 1324 1112 1264 1222.28 1257 1188 0.953 -0.07 0.627334194643552 0.684132682312554 0.0056 0.0098 0.0091 0.0091 TRUE NA NA
+feat0013 1663 1269 149 582 674 752 569 635 657.82 713 602 0.854 -0.227 0.169838645673078 0.22147840244499 0.0043 0.0129 0.0115 0.0115 TRUE NA NA
+feat0014 4406 2749 180 589 1787 1629 688 643 1186.78 1708 666 0.393 -1.347 1.71373115477463e-20 1.75205601922702e-19 0.0029 0.0099 0.0086 0.0086 TRUE NA NA
+feat0015 1703 1065 121 457 691 631 462 499 570.79 661 480 0.736 -0.441 0.00980452226009615 0.0165938548810967 0 0.014 0.012 0.012 TRUE NA NA
+feat0016 5355 4114 577 2218 2172 2438 2205 2421 2309.07 2305 2313 1.007 0.01 0.938883543814683 0.951058415401352 0.0051 0.0081 0.0075 0.0075 TRUE NA NA
+feat0017 14929 9447 739 2554 6055 5599 2824 2788 4316.51 5827 2806 0.485 -1.045 1.17780073804006e-19 1.13220845140625e-18 0.0017 0.0072 0.006 0.006 TRUE NA NA
+feat0018 3169 2279 444 1522 1285 1351 1697 1661 1498.53 1318 1679 1.269 0.344 0.00818279452160768 0.014077135924921 0 0.0091 0.0074 0.0074 TRUE NA NA
+feat0019 5456 4062 445 1567 2213 2408 1701 1710 2007.85 2310 1706 0.741 -0.432 0.000632633357501871 0.0013176722739995 0.002 0.0084 0.0071 0.0071 TRUE NA NA
+feat0020 9338 6881 650 2420 3787 4078 2484 2641 3247.79 3932 2562 0.656 -0.608 3.28482909288193e-07 1.07394290456432e-06 0.0017 0.0075 0.0064 0.0064 TRUE NA NA
+feat0021 7675 6038 961 3697 3113 3579 3673 4035 3599.85 3346 3854 1.153 0.205 0.100350704614807 0.138518059586676 0.0065 0.0074 0.0073 0.0073 TRUE NA NA
+feat0022 4253 2845 326 1495 1725 1686 1246 1632 1572.2 1706 1439 0.855 -0.226 0.126779062818878 0.171123022888893 0.0168 0.009 0.0099 0.0099 TRUE NA NA
+feat0023 9504 7828 494 1892 3855 4640 1888 2065 3111.83 4248 1976 0.472 -1.084 4.25038192544576e-16 3.19911814519519e-15 0.0098 0.0076 0.0081 0.0081 TRUE NA NA
+feat0024 3039 2655 268 1079 1233 1574 1024 1178 1252.03 1404 1101 0.794 -0.333 0.0357410690108382 0.0542897189468009 0.018 0.0097 0.0113 0.0113 TRUE NA NA
+feat0025 3703 2787 477 1955 1502 1652 1823 2134 1777.63 1577 1978 1.258 0.331 0.0149711165549329 0.024458396710861 0.0073 0.0086 0.0084 0.0084 TRUE NA NA
+feat0026 2169 1719 359 1314 880 1019 1372 1434 1176.19 950 1403 1.473 0.559 0.000100797006096178 0.000236102681528341 0.0057 0.0099 0.0091 0.0091 TRUE NA NA
+feat0027 6611 4630 853 3233 2681 2744 3260 3529 3053.54 2712 3394 1.251 0.323 0.00598377988474123 0.0105305102696037 0.001 0.0076 0.0063 0.0063 TRUE NA NA
+feat0028 10881 8152 1620 6008 4413 4832 6191 6557 5498.4 4622 6374 1.376 0.461 5.09216359828929e-05 0.000125448708854365 0.0025 0.0069 0.0061 0.0061 TRUE NA NA
+feat0029 24362 18378 5975 17707 9881 10893 22835 19327 15733.74 10387 21081 2.013 1.009 3.11402648286207e-17 2.53854681672829e-16 0.0092 0.0064 0.0069 0.0069 TRUE NA NA
+feat0030 12087 9876 2455 9159 4902 5854 9382 9997 7533.73 5378 9690 1.791 0.841 4.89831858032855e-12 2.69206771156582e-11 0.0085 0.0067 0.0071 0.0071 TRUE NA NA
+feat0031 2403 1939 687 2591 975 1149 2626 2828 1894.35 1062 2727 2.542 1.346 2.34191754121593e-23 2.87241898424136e-22 0.0068 0.0085 0.0084 0.0084 TRUE NA NA
+feat0032 6349 5345 1126 4425 2575 3168 4303 4830 3719.01 2872 4566 1.584 0.664 7.21144449896223e-07 2.26299853504876e-06 0.0134 0.0073 0.0085 0.0085 TRUE NA NA
+feat0033 6894 4943 1636 5734 2796 2930 6252 6258 4559.16 2863 6255 2.17 1.118 6.14343104496548e-24 7.82120983984055e-23 5e-04 0.0071 0.0057 0.0057 TRUE NA NA
+feat0034 7966 5390 1522 6214 3231 3195 5817 6782 4756.15 3213 6300 1.951 0.964 7.33169506410268e-16 5.38728935943106e-15 0.0054 0.0071 0.0067 0.0067 TRUE NA NA
+feat0035 4553 2926 415 1661 1847 1734 1586 1813 1744.95 1790 1700 0.955 -0.066 0.617200965409598 0.674544820386529 0.0036 0.0087 0.0079 0.0079 TRUE NA NA
+feat0036 3536 2344 593 2433 1434 1389 2266 2656 1936.31 1412 2461 1.739 0.798 1.3055673340174e-09 5.66590872141533e-09 0.0054 0.0084 0.0079 0.0079 TRUE NA NA
+feat0037 8635 7153 402 1495 3502 4240 1536 1632 2727.47 3871 1584 0.415 -1.267 7.158675460754e-21 7.49007838195405e-20 0.0091 0.0078 0.0082 0.0082 TRUE NA NA
+feat0038 4477 3444 300 1052 1816 2041 1147 1148 1537.95 1928 1148 0.6 -0.738 5.70027285243841e-08 2.03379057173775e-07 0.0038 0.009 0.008 0.008 TRUE NA NA
+feat0039 6440 5132 596 2329 2612 3042 2278 2542 2618.37 2827 2410 0.857 -0.222 0.0914980839680359 0.127474345559362 0.008 0.0078 0.0079 0.0079 TRUE NA NA
+feat0040 5485 4982 547 2128 2225 2953 2091 2323 2397.65 2589 2207 0.857 -0.222 0.13850979263415 0.184970919756742 0.0217 0.008 0.0105 0.0105 TRUE NA NA
+feat0041 3402 2896 247 897 1380 1716 944 979 1254.82 1548 962 0.628 -0.671 1.09634990444019e-05 2.96412343115787e-05 0.0127 0.0097 0.0103 0.0103 TRUE NA NA
+feat0042 1044 469 188 525 423 278 718 573 498.23 350 646 1.781 0.833 0.000102943217306734 0.000240919466681204 0.0513 0.0151 0.0212 0.0212 TRUE NA NA
+feat0043 36527 36221 6038 22662 14814 21469 23076 24735 21023.37 18142 23906 1.312 0.392 0.00863444628555805 0.0148003312342565 0.0347 0.0063 0.011 0.011 TRUE NA NA
+feat0044 4504 2857 327 1305 1827 1693 1250 1424 1548.54 1760 1337 0.767 -0.382 0.00508691087048169 0.00907120675174994 0.0044 0.009 0.0082 0.0082 TRUE NA NA
+feat0045 7438 5715 476 1364 3017 3387 1819 1489 2427.98 3202 1654 0.517 -0.951 5.34461197782987e-12 2.92734839847645e-11 0.0124 0.008 0.0086 0.0086 TRUE NA NA
+feat0046 10250 6115 728 2932 4157 3624 2782 3200 3440.99 3890 2991 0.774 -0.37 0.0041329469970869 0.00749294536695835 0.009 0.0074 0.0077 0.0077 TRUE NA NA
+feat0047 9183 4952 869 2153 3724 2935 3321 2350 3082.63 3330 2836 0.849 -0.236 0.149834666692416 0.198349741396378 0.0426 0.0076 0.0129 0.0129 TRUE NA NA
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+feat0051 5450 3574 879 2924 2210 2118 3359 3191 2719.87 2164 3275 1.504 0.589 6.42136348127104e-07 2.03410592796483e-06 6e-04 0.0078 0.0064 0.0064 TRUE NA NA
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diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_T4vsT0.complete.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SARTools_DESeq2_T4vsT0.complete.txt Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,10161 @@
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diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_T8vsT0.complete.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SARTools_DESeq2_T8vsT0.complete.txt Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,10161 @@
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diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_T8vsT4.complete.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SARTools_DESeq2_T8vsT4.complete.txt Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,10161 @@
+Id T0-1 T0-5 T0-6 T4-1 T4-2 T4-3 T8-1 T8-2 T8-3 norm.T0-1 norm.T0-5 norm.T0-6 norm.T4-1 norm.T4-2 norm.T4-3 norm.T8-1 norm.T8-2 norm.T8-3 baseMean T0 T4 T8 FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks outlier
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diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_targetT048_tables.html
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@@ -0,0 +1,22 @@
+
+
+
+
+
+
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+ Galaxy Tool SARTools_DESeq2
+Run at 14/04/2015 14:26:02
+Tables available for downloading
+
+
\ No newline at end of file
diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_target_tables.html
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+ Galaxy Tool SARTools_DESeq2
+Run at 14/04/2015 14:15:36
+Tables available for downloading
+
+
\ No newline at end of file
diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_KOvsWT.complete.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SARTools_edgeR_KOvsWT.complete.txt Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,8218 @@
+Id WT1 WT2 KO1 KO2 norm.WT1 norm.WT2 norm.KO1 norm.KO2 baseMean WT KO FC log2FoldChange pvalue padj tagwise.dispersion trended.dispersion
+feat0001 2728 1636 668 2378 1477 1291 3408 3446 2405.56 1384 3427 2.475 1.307 7.79599543765362e-26 1.05831303253472e-24 0.0066 0.0067
+feat0002 3169 1892 376 1228 1716 1493 1918 1780 1726.7 1604 1849 1.147 0.198 0.130545989349202 0.170384470102199 0.0071 0.0075
+feat0003 2784 1626 622 2117 1508 1283 3173 3068 2257.94 1396 3120 2.231 1.158 1.28625215680723e-19 1.14197945395106e-18 0.007 0.0068
+feat0004 6311 4283 374 1470 3418 3379 1908 2130 2708.84 3398 2019 0.598 -0.742 6.38828918161185e-10 2.62901399067368e-09 0.006 0.0066
+feat0005 12769 9132 718 3199 6915 7205 3663 4636 5604.8 7060 4150 0.591 -0.758 7.60645615828879e-09 2.76804019849896e-08 0.0078 0.007
+feat0006 3953 2867 666 2579 2141 2262 3398 3738 2884.5 2202 3568 1.627 0.702 2.38863904781785e-09 9.24653217780584e-09 0.006 0.0066
+feat0007 4070 2498 310 1039 2204 1971 1581 1506 1815.57 2088 1544 0.737 -0.441 0.000570823894492269 0.00112725654976982 0.0067 0.0073
+feat0008 2750 2026 257 924 1489 1598 1311 1339 1434.49 1544 1325 0.86 -0.218 0.0958207230159633 0.128802610948291 0.0069 0.0083
+feat0009 2044 1286 118 400 1107 1015 602 580 825.82 1061 591 0.555 -0.85 1.85178214020667e-07 5.76552912929317e-07 0.0099 0.0121
+feat0010 3118 2361 511 1885 1689 1863 2607 2732 2222.52 1776 2670 1.507 0.592 1.02538994188499e-06 2.93416438406299e-06 0.0062 0.0068
+feat0011 9296 4990 501 1705 5034 3937 2556 2471 3499.55 4486 2514 0.559 -0.838 8.82828539823182e-10 3.57946026212712e-09 0.0082 0.0066
+feat0012 2933 2233 291 1158 1588 1762 1485 1678 1628.24 1675 1582 0.952 -0.071 0.58779948131871 0.640891567145058 0.0072 0.0077
+feat0013 1663 1269 149 582 901 1001 760 843 876.35 951 802 0.851 -0.233 0.142926841736404 0.184305888476753 0.01 0.0116
+feat0014 4406 2749 180 589 2386 2169 918 854 1581.73 2278 886 0.386 -1.373 4.23989480255885e-24 5.14936842051231e-23 0.0069 0.0078
+feat0015 1703 1065 121 457 922 840 617 662 760.53 881 640 0.73 -0.454 0.0062313222294616 0.0104073416618448 0.0106 0.0128
+feat0016 5355 4114 577 2218 2900 3246 2944 3214 3075.98 3073 3079 1.006 0.008 0.944853812345459 0.954238888593029 0.0064 0.0065
+feat0017 14929 9447 739 2554 8085 7454 3770 3701 5752.48 7770 3736 0.48 -1.057 1.69770028833938e-19 1.4972511966452e-18 0.006 0.007
+feat0018 3169 2279 444 1522 1716 1798 2265 2206 1996.28 1757 2236 1.271 0.346 0.00379338905209705 0.00657868103541138 0.006 0.0071
+feat0019 5456 4062 445 1567 2955 3205 2270 2271 2675.19 3080 2270 0.737 -0.439 0.000218387882478178 0.000458626083715393 0.006 0.0066
+feat0020 9338 6881 650 2420 5057 5429 3316 3507 4327.31 5243 3412 0.652 -0.617 6.87264841393329e-08 2.25451208795214e-07 0.0057 0.0067
+feat0021 7675 6038 961 3697 4157 4764 4903 5358 4795.19 4460 5130 1.153 0.205 0.0888402705782257 0.12037546456307 0.0066 0.0068
+feat0022 4253 2845 326 1495 2303 2245 1663 2167 2094.41 2274 1915 0.853 -0.23 0.0932231524996643 0.125714558083545 0.0081 0.0069
+feat0023 9504 7828 494 1892 5147 6176 2520 2742 4146.32 5662 2631 0.466 -1.1 7.5045755019466e-18 5.85283314882208e-17 0.0071 0.0067
+feat0024 3039 2655 268 1079 1646 2095 1367 1564 1667.87 1870 1466 0.79 -0.341 0.0225952216735988 0.0343418013781962 0.0095 0.0076
+feat0025 3703 2787 477 1955 2005 2199 2433 2833 2367.74 2102 2633 1.261 0.335 0.00785544754854683 0.0129325507551097 0.0069 0.0067
+feat0026 2169 1719 359 1314 1175 1356 1831 1904 1566.66 1266 1868 1.48 0.566 1.94447531192018e-05 4.72603150208525e-05 0.0073 0.0079
+feat0027 6611 4630 853 3233 3580 3653 4352 4685 4067.56 3616 4518 1.252 0.325 0.00331405742323332 0.00581971894079935 0.0054 0.0066
+feat0028 10881 8152 1620 6008 5893 6432 8265 8707 7324 6162 8486 1.378 0.463 9.68500985305593e-05 0.00021411978141208 0.0065 0.0074
+feat0029 24362 18378 5975 17707 13194 14500 30482 25661 20959.17 13847 28072 2.026 1.019 2.88687014209753e-13 1.59368854825717e-12 0.0091 0.0089
+feat0030 12087 9876 2455 9159 6546 7792 12524 13273 10033.9 7169 12898 1.8 0.848 1.14922252740989e-10 5.08740412106047e-10 0.008 0.0079
+feat0031 2403 1939 687 2591 1301 1530 3505 3755 2522.73 1416 3630 2.572 1.363 9.50636450041952e-27 1.39013105883892e-25 0.0069 0.0067
+feat0032 6349 5345 1126 4425 3438 4217 5744 6413 4953.16 3828 6078 1.592 0.671 3.25843225792036e-07 9.84086128008976e-07 0.0079 0.0068
+feat0033 6894 4943 1636 5734 3734 3900 8346 8310 6072.37 3817 8328 2.182 1.126 2.41245967268691e-22 2.61816053154494e-21 0.006 0.0071
+feat0034 7966 5390 1522 6214 4314 4253 7765 9005 6334.18 4284 8385 1.962 0.972 3.29319012042412e-15 2.10758868929798e-14 0.0069 0.0072
+feat0035 4553 2926 415 1661 2466 2309 2117 2407 2324.65 2388 2262 0.954 -0.069 0.576324316722394 0.630020604579723 0.0064 0.0068
+feat0036 3536 2344 593 2433 1915 1849 3025 3526 2578.88 1882 3276 1.75 0.807 4.53683717266055e-11 2.0885728997983e-10 0.0065 0.0066
+feat0037 8635 7153 402 1495 4676 5644 2051 2167 3634.35 5160 2109 0.41 -1.287 4.69783068469199e-23 5.35404628892905e-22 0.0072 0.0066
+feat0038 4477 3444 300 1052 2425 2717 1530 1525 2049.22 2571 1528 0.594 -0.751 2.19040743088845e-09 8.51646681951008e-09 0.0064 0.007
+feat0039 6440 5132 596 2329 3488 4049 3041 3375 3488.12 3768 3208 0.855 -0.226 0.0672581095710166 0.0933260529630974 0.0068 0.0066
+feat0040 5485 4982 547 2128 2970 3931 2791 3084 3193.92 3450 2938 0.854 -0.227 0.115235265499144 0.152199325426812 0.0094 0.0065
+feat0041 3402 2896 247 897 1842 2285 1260 1300 1671.83 2064 1280 0.622 -0.685 1.62434624517133e-06 4.54508419990783e-06 0.0084 0.0076
+feat0042 1044 469 188 525 565 370 959 761 663.84 468 860 1.816 0.861 0.000132405493783312 0.000287311975735473 0.0215 0.014
+feat0043 36527 36221 6038 22662 19782 28578 30803 32842 28001.22 24180 31822 1.316 0.397 0.0194165949326836 0.0298298595383349 0.0137 0.0093
+feat0044 4504 2857 327 1305 2439 2254 1668 1891 2063.19 2346 1780 0.764 -0.388 0.00189978503493442 0.00346640350469629 0.0065 0.007
+feat0045 7438 5715 476 1364 4028 4509 2428 1977 3235.57 4268 2202 0.511 -0.968 2.37668736210636e-13 1.31936831580991e-12 0.0075 0.0065
+feat0046 10250 6115 728 2932 5551 4825 3714 4249 4584.68 5188 3982 0.77 -0.376 0.00245357228761566 0.00440093969514827 0.007 0.0068
+feat0047 9183 4952 869 2153 4973 3907 4433 3120 4108.42 4440 3776 0.845 -0.243 0.142522304913014 0.183903476980215 0.0126 0.0066
+feat0048 10881 7247 1080 3366 5893 5718 5510 4878 5499.57 5806 5194 0.892 -0.165 0.161080152413612 0.205186967566098 0.0063 0.007
+feat0049 7853 4816 725 2602 4253 3800 3699 3771 3880.54 4026 3735 0.928 -0.108 0.34878554757062 0.408087811578803 0.0059 0.0066
+feat0050 9532 5400 856 2303 5162 4261 4367 3338 4281.8 4712 3852 0.813 -0.299 0.0408628505510545 0.0590488603330861 0.0098 0.0067
+feat0051 5450 3574 879 2924 2952 2820 4484 4237 3623.29 2886 4360 1.508 0.593 1.50231918411264e-07 4.74432279063759e-07 0.0056 0.0066
+feat0052 2764 2082 462 1433 1497 1643 2357 2077 1893.3 1570 2217 1.404 0.49 0.000134221940956685 0.000290856861975056 0.0069 0.0072
+feat0053 9621 4999 1491 4811 5210 3944 7606 6972 5933.29 4577 7289 1.59 0.669 3.14840597118924e-06 8.5015510864937e-06 0.0095 0.0071
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diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_KOvsWT_small.complete.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SARTools_edgeR_KOvsWT_small.complete.txt Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,11 @@
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diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_T4vsT0.complete.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SARTools_edgeR_T4vsT0.complete.txt Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,10161 @@
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