Mercurial > repos > lgueguen > sartools
changeset 0:581d217c7337 draft
Planemo upload
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--- /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 +----------------------------------------------------------- + +[](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: +------------------------- +[](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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_sartools_deseq2.xml Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,194 @@ +<tool id="sartools_deseq2" name="SARTools DESeq2" version="1.0.0"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description>Compare two or more biological conditions in a RNA-Seq framework with DESeq2</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + <!-- [REQUIRED] The command to execute --> + <command interpreter="python"><![CDATA[ + + abims_sartools_deseq2_wrapper.py + ## parameters + @COMMAND_BASIC_PARAMETERS@ + #if str( $advanced_parameters.adv_param ) == "show": + @COMMAND_BATCH_PARAM@ + --fitType $advanced_parameters.fitType + --cooksCutoff $advanced_parameters.cooksCutoff + --independentFiltering $advanced_parameters.independentFiltering + --alpha $advanced_parameters.alpha + --pAdjustMethod $advanced_parameters.pAdjustMethod + --typeTrans $advanced_parameters.typeTrans + --locfunc $advanced_parameters.locfunc + --colors $advanced_parameters.colors + #end if + ## ouputs + @COMMAND_OUTPUTS@ + + ]]></command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + + <expand macro="basic_parameters" /> + + <conditional name="advanced_parameters" > + <param name="adv_param" type="select" label="Advanced Parameters" help="" > + <option value="hide" selected="true">Hide</option> + <option value="show">Show</option> + </param> + <when value="hide" /> + <when value="show"> + <expand macro="batch_param" /> + <param name="fitType" type="select" label="Mean-variance relationship" help="(-f, --fitType) Type of model for the mean-dispersion relationship. Parametric by default." > + <option value="parametric" selected="true">parametric</option> + <option value="local">local</option> + </param> + <param name="cooksCutoff" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" help="(-o, --cooksCutoff) Checked by default."/> + <param name="independentFiltering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" help="(-i, --independentFiltering) Checked by default."/> + <expand macro="alpha_param" /> + <expand macro="padjustmethod_param" /> + <param name="typeTrans" type="select" label="Transformation for PCA/clustering" help="(-T --typeTrans) Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." > + <option value="VST" selected="true">VST</option> + <option value="rlog">rlog</option> + </param> + <param name="locfunc" type="select" label="Estimation of the size factors" help="(-l --locfunc) 'median' (default) or 'shorth' from the genefilter package." > + <option value="median" selected="true">median</option> + <option value="shorth">shorth</option> + </param> + <expand macro="colors_param" /> + </when> + </conditional> + + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + + <expand macro="outputs" /> + + </outputs> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + <test> + <!-- Test with 2 conditions, 2 replicates, 8217 features --> + <param name="targetFile" dbkey="?" value="target.txt" /> + <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/> + <param name="adv_param" value="show"/> + <output name="log"> + <assert_contents> + <has_text text="KO vs WT 0.1 171" /> + <has_text text="KO vs WT 2584 2665 5249" /> + <has_text text="HTML report created" /> + </assert_contents> + </output> + </test> +<!-- <test> +--> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect --> +<!-- <param name="targetFile" dbkey="?" value="targetT048.txt" /> + <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/> + <param name="condRef" value="T0"/> + <param name="adv_param" value="show"/> + <param name="condition" value="true"/> + <output name="tables_html" file="SARTools_DESeq2_targetT048_tables.html" lines_diff="14"> + <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_DESeq2_T4vsT0.complete.txt"/> + <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_DESeq2_T8vsT0.complete.txt"/> + <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_DESeq2_T8vsT4.complete.txt"/> + </output> + </test> +--> </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help><![CDATA[ + +@HELP_AUTHORS@ + +=============== +SARTools DESeq2 +=============== + +----------- +Description +----------- + +@HELP_DESCRIPTION@ + + +----------- +Input files +----------- + +@HELP_INPUT_FILES@ + + +---------- +Parameters +---------- + + @HELP_BASIC_PARAMETERS@ + * **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account); + * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05); + * **fitType:** type of model for the mean-dispersion relationship ("parametric" by default, or "local"); + * **cooksCutoff:** TRUE (default) of FALSE to execute or not the detection of the outliers [4]; + * **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5]; + * **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods); + * **typeTrans:** method of transformation of the counts for the clustering and the PCA (default is "VST" for Variance Stabilizing Transformation, or "rlog" for Regularized Log Transformation); + * **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package); + * **colors:** colors used for the figures (one per biological condition), 8 are given by default. + + +------------ +Output files +------------ + +@HELP_OUTPUT_FILES@ + + +--------------------------------------------------- + +[1] G.-K. Smyth. Limma: linear models for microarray data. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber, editors, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pages 397–420. Springer, New York, 2005. + +[2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011. + +[3] S. Anders, P.-T. Pyl, and W. Huber. HTSeq - A Python framework to work with high-throughput sequencing data. bioRxiv preprint, 2014. URL: http://dx.doi.org/10.1101/002824. + +[4] R.-D. Cook. Detection of Influential Observation in Linear Regression. Technometrics, February 1977. + +[5] R. Bourgon, R. Gentleman, and W. Huber. Independent filtering increases detection power for high-throughput experiments. PNAS, 107(21):9546–9551, 2010. URL: http://www.pnas.org/content/107/21/9546.long. + +[6] Y. Benjamini and Y. Hochberg. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, 57:289–300, 1995. + +[7] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165–1188, 2001. + + + ]]></help> + + <citations> + <expand macro="common_citations" /> + <citation type="bibtex">@ARTICLE{Cook77, + author = {R.-D. Cook}, + title = {Detection of Influential Observation in Linear Regression}, + journal = {Technometrics}, + year = {1977}, + month = {February} + }</citation> + <citation type="bibtex">@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} + }</citation> + </citations> + +</tool>
--- /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() + +
--- /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 @@ +<tool id="sartools_edger" name="SARTools edgeR" version="1.0.0"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description>Compare two or more biological conditions in a RNA-Seq framework with edgeR</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + + <!-- [REQUIRED] The command to execute --> + <command interpreter="python"><![CDATA[ + + abims_sartools_edger_wrapper.py + ## parameters + @COMMAND_BASIC_PARAMETERS@ + #if str( $advanced_parameters.adv_param ) == "show": + @COMMAND_BATCH_PARAM@ + --alpha $advanced_parameters.alpha + --pAdjustMethod $advanced_parameters.pAdjustMethod + --cpmCutoff $advanced_parameters.cpmCutoff + --geneSelection $advanced_parameters.geneSelection + --normalizationMethod $advanced_parameters.normalizationMethod + --colors $advanced_parameters.colors + #end if + ## ouputs + @COMMAND_OUTPUTS@ + + ]]></command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + + <expand macro="basic_parameters" /> + + <conditional name="advanced_parameters" > + <param name="adv_param" type="select" label="Advanced Parameters" help="" > + <option value="hide" selected="true">Hide</option> + <option value="show">Show</option> + </param> + <when value="hide" /> + <when value="show"> + <expand macro="batch_param" /> + <expand macro="alpha_param" /> + <expand macro="padjustmethod_param" /> + <param name="cpmCutoff" type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" help="(-m, --cpmCutoff) Set to 0 to disable filtering. Default is 1." /> + <param name="geneSelection" type="select" label="Selection of the features in MDSPlot" help="(-g, --gene.selection) Default is 'pairwise'." > + <option value="pairwise" selected="true">pairwise</option> + <option value="common">common</option> + </param> + <param name="normalizationMethod" type="select" label="Normalization method in calcNormFactors" help="(-n, --normalizationMethod) 'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." > + <option value="TMM" selected="true">TMM</option> + <option value="RLE">RLE</option> + <option value="upperquartile">upperquartile</option> + </param> + <expand macro="colors_param" /> + </when> + </conditional> + + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + + <expand macro="outputs" /> + + </outputs> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + <test> + <!-- Test with 2 conditions, 2 replicates, 10 features --> + <param name="targetFile" dbkey="?" value="target_small.txt" /> + <param name="rawDir" value="raw_small.zip" dbkey="?" ftype="zip"/> + <param name="adv_param" value="show"/> + <output name="log"> + <assert_contents> + <has_text text="KO vs WT 5 4 9" /> + <has_text text="HTML report created" /> + </assert_contents> + </output> + </test> +<!-- <test> +--> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10 features, with batch effect --> +<!-- <param name="targetFile" dbkey="?" value="targetT048_small.txt" /> + <param name="rawDir" value="rawT048_small.zip" dbkey="?" ftype="no_unzip.zip"/> + <param name="condRef" value="T0"/> + <param name="adv_param" value="show"/> + <param name="condition" value="true"/> + <output name="tables_html" file="SARTools_edgeR_targetT048_small_tables.html" lines_diff="12"> + <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0_small.complete.txt"/> + <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0_small.complete.txt"/> + <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4_small.complete.txt"/> + </output> + </test> +--> <test> + <!-- Test with 2 conditions, 2 replicates, 8217 features --> + <param name="targetFile" dbkey="?" value="target.txt" /> + <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/> + <param name="adv_param" value="show"/> + <output name="log"> + <assert_contents> + <has_text text="KO vs WT 2691 2713 5404" /> + <has_text text="HTML report created" /> + </assert_contents> + </output> + </test> +<!-- <test> +--> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect --> +<!-- <param name="targetFile" dbkey="?" value="targetT048.txt" /> + <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/> + <param name="condRef" value="T0"/> + <param name="adv_param" value="show"/> + <param name="condition" value="true"/> + <output name="tables_html" file="SARTools_edgeR_targetT048_tables.html" lines_diff="14"> + <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0.complete.txt"/> + <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0.complete.txt"/> + <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4.complete.txt"/> + </output> + </test> +--> </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help><![CDATA[ + +@HELP_AUTHORS@ + +============== +SARTools edgeR +============== + +----------- +Description +----------- + +@HELP_DESCRIPTION@ + + +----------- +Input files +----------- + +@HELP_INPUT_FILES@ + + +---------- +Parameters +---------- + + @HELP_BASIC_PARAMETERS@ + * **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account); + * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05); + * **pAdjustMethod:** p-value adjustment method for multiple testing [4, 5] ("BH" by default, "BY" or any value of p.adjust.methods); + * **cpmCutoff:** counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering); + * **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common); + * **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile"; + * **colors:** colors used for the figures (one per biological condition), 8 are given by default. + + +------------ +Output files +------------ + +@HELP_OUTPUT_FILES@ + + +--------------------------------------------------- + +[1] G.-K. Smyth. Limma: linear models for microarray data. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber, editors, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pages 397–420. Springer, New York, 2005. + +[2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011. + +[3] S. Anders, P.-T. Pyl, and W. Huber. HTSeq - A Python framework to work with high-throughput sequencing data. bioRxiv preprint, 2014. URL: http://dx.doi.org/10.1101/002824. + +[4] Y. Benjamini and Y. Hochberg. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, 57:289–300, 1995. + +[5] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165–1188, 2001. + + + ]]></help> + + <citations> + <expand macro="common_citations" /> + </citations> + +</tool>
--- /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() + +
--- /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 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2.0">r-sartools</requirement> + <requirement type="package" version="1.3.0">r-optparse</requirement> + </requirements> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1" level="fatal" /> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted" /> + <regex match="rsync error" + source="both" + level="fatal" + description="rsync error" /> + </stdio> + </xml> + + <token name="@COMMAND_BASIC_PARAMETERS@"> + --projectName $projectName + --author $author + --targetFile $targetFile + --rawDir $rawDir + --featuresToRemove $featuresToRemove + --varInt $varInt + --condRef $condRef + </token> + + <token name="@COMMAND_BATCH_PARAM@"> + #if $advanced_parameters.batch_condition.condition: + --batch $advanced_parameters.batch_condition.batch + #else: + --batch NULL + #end if + </token> + + <token name="@COMMAND_OUTPUTS@"> + --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 + </token> + + <macro name="basic_parameters"> + <param name="projectName" type="text" value="Project" label="Name of the project used for the report" help="(-P, --projectName) No space allowed." > + <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> + </param> + <param name="author" type="text" value="Galaxy" label="Name of the report author" help="(-A, --author) No space allowed." > + <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> + </param> + <param name="targetFile" type="data" format="txt" label="Design / target file" help="(-t, --targetFile) See the help section below for details on the required format." /> + <param name="rawDir" type="data" format="no_unzip.zip,zip" label="Zip file containing raw counts files" help="(-r, --rawDir) See the help section below for details on the required format." /> + <param name="featuresToRemove" type="text" size="100" value="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual" label="Names of the features to be removed" help="(-F, --featuresToRemove) Separate the features with a comma, no space allowed. More than once can be specified. Specific HTSeq-count information and rRNA for example. Default are 'alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual'." > + <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> + </param> + <param name="varInt" type="text" value="group" label="Factor of interest" help="(-v, --varInt) Biological condition in the target file. Default is 'group'." > + <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> + </param> + <param name="condRef" type="text" value="WT" label="Reference biological condition" help="(-c, --condRef) Reference biological condition used to compute fold-changes, must be one of the levels of 'Factor of interest'." > + <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> + </param> + </macro> + + <macro name="batch_param"> + <conditional name="batch_condition"> + <param name="condition" type="boolean" checked="false" truevalue="batch" falsevalue="NULL" label="Add a blocking factor" help="(-b, --batch) Adjustment variable to use as a batch effect. Default: unchecked if no batch effect needs to be taken into account."/> + <when value="NULL" /> + <when value="batch"> + <param name="batch" type="text" value="batch" label="Blocking factor value" help="Must be a column of the target file" > + <validator type="empty_field"/> + </param> + </when> + </conditional> + </macro> + + <macro name="alpha_param"> + <param name="alpha" type="float" value="0.05" min="0" max="1" label="Threshold of statistical significance" help="(-a, --alpha) Significance threshold applied to the adjusted p-values to select the differentially expressed features. Default is 0.05. The comma is not allowed as decimal separator, use a point instead." /> + </macro> + + <macro name="padjustmethod_param"> + <param name="pAdjustMethod" type="select" label="p-value adjustment method" help="(-p, --pAdjustMethod) p-value adjustment method for multiple testing. 'BH' by default, 'BY' or any value of p.adjust.methods." > + <option value="BH" selected="true">BH</option> + <option value="BY">BY</option> + <option value="bonferroni">bonferroni</option> + <option value="fdr">fdr</option> + <option value="hochberg">hochberg</option> + <option value="holm">holm</option> + <option value="hommel">hommel</option> + </param> + </macro> + + <macro name="colors_param"> + <param name="colors" type="text" size="100" value="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange" label="Colors of each biological condition on the plots: 'col1,col2,col3,col4'" help="(-C, --colors) Separate the colors with a comma, no space allowed. Default are 'dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange'." > + <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> + </param> + </macro> + + <macro name="outputs"> + <data name="report_html" format="html" label="${tool.name} report" /> + <data name="tables_html" format="html" label="${tool.name} tables" /> + <data name="figures_html" format="html" label="${tool.name} figures" /> + <data name="log" format="txt" label="${tool.name} R log" /> + <data name="rdata" format="data" label="${tool.name} R objects (.RData)" /> + </macro> + + <token name="@HELP_AUTHORS@"> +.. 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. + +--------------------------------------------------- + </token> + + <token name="@HELP_DESCRIPTION@"> + | 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. + </token> + + <token name="@HELP_INPUT_FILES@"> +.. 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). + </token> + + <token name="@HELP_BASIC_PARAMETERS@"> + * **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); + </token> + + <token name="@HELP_OUTPUT_FILES@"> +**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. + </token> + + <macro name="common_citations"> + <citation type="doi">10.1371/journal.pone.0157022</citation> + <citation type="bibtex">@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} + }</citation> + <citation type="doi">10.1093/bioinformatics/btu638</citation> + <citation type="bibtex">@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} + }</citation> + <citation type="bibtex">@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} + }</citation> + </macro> + +</macros>
--- /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="""<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8" /> + <title></title> + </head> + <body> + <h1>Galaxy Tool %s</h1> +""" %(tool) + +fin_html="</body></html>" + +html=debut_html +run_date=time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) +html+='<div>Run at %s</div><br/>\n'%run_date +html+='<div><strong>%s</strong> available for downloading</div><br/>\n'%output_type + + +flist = os.listdir(output_dir) +flist.sort() + + +html+='<div><table cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n' + +for f in flist : + size=getfSize(f,output_dir) + html+='<tr><td><a href="%s">%s</a></td><td>%s</td></tr>\n'%(f,f,size) +html+='</table></div><br/>\n' + +html+=fin_html + +htmlf = file(output_html,'w') +htmlf.write(html) +htmlf.close()
--- /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__()
--- /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 @@ +<tool id="presartools" name="Preprocess files for SARTools" version="0.1.0"> + <description>generate design/target file and archive for SARTools inputs</description> + <command interpreter="python"> + 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 + + </command> + <inputs> + <conditional name="batch_condition"> + <param name="condition" type="boolean" checked="false" truevalue="batch" falsevalue="NULL" label="Add a blocking factor" help="Adjustment variable to use as a batch effect (default no)."/> + <when value="NULL"> + <repeat name="levels" title="Group" min="2"> + <param name="level_name" type="text" format="txt" value="group1" label="Group name"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + <mapping initial="none"> + <add source=" " target="_"/> + </mapping> + </sanitizer> + </param> + <repeat name="rep_counts" title="Raw counts" min="2"> + <param name="count_data" type="data" format="txt" label="Replicate raw count"/> + <param name="label" format="txt" type="text" value="replicate1" label="Replicate label name" help="You need to specify an unique label name for your replicates."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + <mapping initial="none"> + <add source=" " target="_"/> + </mapping> + </sanitizer> + </param> + </repeat> + </repeat> + </when> + <when value="batch"> + <repeat name="levels" title="level" min="2"> + <param name="level_name" type="text" format="txt" value="group1" label="Group name"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + <mapping initial="none"> + <add source=" " target="_"/> + </mapping> + </sanitizer> + </param> + <repeat name="rep_counts" title="Raw counts" min="2"> + <param name="count_data" type="data" format="txt" label="Replicate raw count"/> + <param name="label" format="txt" type="text" value="replicate1" label="Replicate label name" help="You need to specify an unique label name for your replicates."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + <mapping initial="none"> + <add source=" " target="_"/> + </mapping> + </sanitizer> + </param> + <param name="batch_value" format="txt" type="text" value="day1" label="Blocking factor"/> + </repeat> + </repeat> + </when> + </conditional> + </inputs> + + <outputs> + <data format="tabular" name="outfile" label="design file for SARTools (on ${on_string})" /> + <data format="no_unzip.zip" name="outarch" label="counts files for SARTools (on ${on_string})"/> + </outputs> + <tests> + <test> + <param name="levels_0|level_name" value="group1"/> + <param name="levels_0|rep_counts_0|count_data" value="group1_count1.txt"/> + <param name="levels_0|rep_counts_0|label" value="group1_rep1"/> + <param name="levels_0|rep_counts_1|count_data" value="group1_count2.txt"/> + <param name="levels_0|rep_counts_1|label" value="group1_rep2"/> + <param name="levels_1|level_name" value="group2"/> + <param name="levels_1|rep_counts_0|count_data" value="group2_count1.txt"/> + <param name="levels_1|rep_counts_0|label" value="group2_rep1"/> + <param name="levels_1|rep_counts_1|count_data" value="group2_count2.txt"/> + <param name="levels_1|rep_counts_1|label" value="group2_rep2"/> + <output name="outfile" file="test_output_target.html"/> + </test> + </tests> + <help> +----------- +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 + </help> +</tool>
--- /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 @@ +<?xml version="1.0"?> +<repositories description="SARTools requires the Galaxy applicable data format no_unzip.zip"> + <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories>
--- /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 <hugo.varet@pasteur.fr>") +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)
--- /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 <hugo.varet@pasteur.fr>") +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)
--- /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 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--- /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 @@ +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 +CADAFUBG00000001 151 131 183 31 35 44 19 31 18 104 99 111 37 45 38 26 39 24 58.24 105 40 30 0.383 -1.384 1.86195043494196e-07 2.83755371198831e-07 0 0.0658 0.0344 0.0344 TRUE NA NA +CADAFUBG00000002 142 134 153 650 629 783 136 241 151 98 102 93 783 807 678 187 305 203 361.6 98 756 232 7.704 2.946 4.15025789993673e-51 1.31816284738427e-50 0.0264 0.0206 0.0236 0.0236 TRUE NA NA +CADAFUBG00000003 157 147 166 7 10 20 8 10 8 108 111 101 8 13 17 11 13 11 43.7 107 13 12 0.126 -2.993 3.24447275074574e-17 6.28014898920843e-17 0 0.0837 0.0483 0.0483 TRUE NA NA +CADAFUBG00000004 275 249 342 70 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2133 634 486 762 559 733 493 1362 1326 1292 764 623 660 767 927 662 931.37 1327 682 785 0.515 -0.958 1.78501533268872e-12 3.11054016169832e-12 0.0101 0.0153 0.0123 0.0123 TRUE NA NA +CADAFUBG00000118 1364 1168 1348 12521 12865 14522 11444 11774 10478 942 885 816 15092 16500 12572 15707 14888 14062 10162.78 881 14721 14886 16.651 4.058 0 0 0.0048 0.0122 0.0071 0.0071 TRUE NA NA +CADAFUBG00000119 19439 16792 20554 197588 179259 211069 164633 195024 162504 13423 12730 12448 238164 229907 182720 225963 246606 218093 153339.45 12867 216930 230221 16.77 4.068 0 0 0.0057 0.0119 0.0077 0.0077 TRUE NA NA +CADAFUBG00000120 3251 2814 3402 1547 1458 2667 3946 3409 4797 2245 2133 2060 1865 1870 2309 5416 4311 6438 3182.94 2146 2015 5388 0.937 -0.095 0.538536001705795 0.569607567186399 0.0222 0.0129 0.0166 0.0166 TRUE NA NA +CADAFUBG00000121 1031 945 1107 895 1051 1763 597 642 596 712 716 670 1079 1348 1526 819 812 800 942.53 699 1318 810 1.878 0.909 6.97896447720153e-12 1.20052529345833e-11 0.0097 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223 202 240 274 177.89 29 266 239 9.184 3.199 3.28158438300284e-33 8.31654811090983e-33 0.0454 0.0296 0.0379 0.0379 TRUE NA NA +CADAFUBG00010148 7 6 12 1 2 4 3 1 4 5 5 7 1 3 3 4 1 5 3.85 6 2 3 0.47 -1.09 0.214109213226732 0.23939244920153 0 0.8276 0.3682 0.3682 TRUE NA NA +CADAFUBG00010149 20 21 35 36 15 54 11 8 8 14 16 21 43 19 47 15 10 11 21.81 17 36 12 2.13 1.091 0.0159273696650112 0.0195894167060116 0.0818 0.1559 0.1178 0.1178 TRUE NA NA +CADAFUBG00010150 6 8 11 6 11 8 6 6 4 4 6 7 7 14 7 8 8 5 7.37 6 9 7 1.617 0.693 0.285784862959029 0.314648418237198 0 0.4378 0.2086 0.2086 TRUE NA NA +CADAFUBG00010151 1315 1239 1602 215 574 394 130 367 175 908 939 970 259 736 341 178 464 235 559.03 939 445 292 0.482 -1.052 0.0413750639170558 0.0492422570916648 0.1994 0.0175 0.0996 0.1994 TRUE NA NA +CADAFUBG00010152 22 32 41 51 56 69 19 32 18 15 24 25 61 72 60 26 40 24 38.67 21 64 30 2.964 1.568 3.19685129096871e-06 4.66931783499152e-06 0.0217 0.0931 0.0587 0.0587 TRUE NA NA +CADAFUBG00010153 2949 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0.0259 0.0259 TRUE NA NA +CADAFUBG00010159 45 46 50 7 10 6 1 0 2 31 35 30 8 13 5 1 0 3 14.08 32 9 1 0.275 -1.864 0.000562206876564348 0.000747971166993172 0 0.2348 0.1467 0.1467 TRUE NA NA +CADAFUBG00010160 5 2 3 21 23 29 18 17 20 3 2 2 25 29 25 25 21 27 17.75 2 26 24 10.774 3.43 2.09635470920108e-09 3.39075501668556e-09 0 0.1888 0.091 0.091 TRUE NA NA
--- /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 @@ +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 +CADAFUBG00000001 151 131 183 31 35 44 19 31 18 104 99 111 37 45 38 26 39 24 58.24 105 40 30 0.288 -1.796 3.19254036122059e-10 5.29594789775794e-10 0 0.0658 0.0344 0.0344 TRUE NA NA +CADAFUBG00000002 142 134 153 650 629 783 136 241 151 98 102 93 783 807 678 187 305 203 361.6 98 756 232 2.373 1.247 8.4420077283023e-10 1.38349771025326e-09 0.0264 0.0206 0.0236 0.0236 TRUE NA NA +CADAFUBG00000003 157 147 166 7 10 20 8 10 8 108 111 101 8 13 17 11 13 11 43.7 107 13 12 0.11 -3.182 8.62872166438115e-17 1.67959964813744e-16 0 0.0837 0.0483 0.0483 TRUE NA NA +CADAFUBG00000004 275 249 342 70 44 91 75 64 62 190 189 207 84 56 79 103 81 83 119.16 195 73 89 0.456 -1.132 7.97940126782767e-08 1.23609969370234e-07 0.0052 0.0383 0.0231 0.0231 TRUE NA NA +CADAFUBG00000005 4 5 2 0 0 1 2 2 3 3 4 1 0 0 1 3 3 4 1.99 3 0 3 1.172 0.229 0.834645459654261 0.849614782418351 0 1.5875 0.7414 0.7414 TRUE NA NA +CADAFUBG00000006 2 0 1 0 1 2 7 3 3 1 0 1 0 1 2 10 4 4 2.49 1 1 6 6.468 2.693 0.0205089978411282 0.0251045927028114 0 1.2715 0.7505 0.7505 TRUE NA NA +CADAFUBG00000007 4 7 3 0 0 0 0 0 0 3 5 2 0 0 0 0 0 0 1.1 3 0 0 0.075 -3.737 0.0227978301343105 0.0278304619243673 0 2.8695 1.9114 1.9114 TRUE NA NA +CADAFUBG00000008 10 16 10 28 12 10 16 33 23 7 12 6 34 15 9 22 42 31 19.72 8 19 32 3.673 1.877 0.000690565065722195 0.00091752633914101 0.1724 0.1711 0.1716 0.1716 TRUE NA NA +CADAFUBG00000009 12 20 24 74 84 77 10 10 9 8 15 15 89 108 67 14 13 12 37.78 13 88 13 1.015 0.022 0.960733449551886 0.964574078972441 0.0433 0.095 0.0694 0.0694 TRUE NA NA +CADAFUBG00000010 269 262 379 112 132 138 44 33 48 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25 31 5 5 2 1 0 0 35 32 27 7 6 3 12.27 0 31 5 12.153 3.603 0.000710716516555413 0.000944051054517476 0 0.2678 0.1537 0.1537 TRUE NA NA +CADAFUBG00000102 31 18 31 6 5 6 4 6 4 21 14 19 7 6 5 5 8 5 10.12 18 6 6 0.354 -1.499 0.0115758218980508 0.0143817347004475 0 0.322 0.1464 0.1464 TRUE NA NA +CADAFUBG00000103 2 2 6 8 14 10 26 30 25 1 2 4 10 18 9 36 38 34 16.66 2 12 36 14.505 3.859 2.16677732853042e-10 3.61165505930257e-10 0 0.2003 0.1255 0.1255 TRUE NA NA +CADAFUBG00000104 1 1 0 10 10 5 100 114 116 1 1 0 12 13 4 137 144 156 51.97 1 10 146 207.564 7.697 3.05049188057044e-21 6.47343503004027e-21 0 0.0723 0.0618 0.0618 TRUE NA NA +CADAFUBG00000105 2447 2124 2580 7637 6664 7497 3974 5722 4218 1690 1610 1562 9205 8547 6490 5454 7235 5661 5272.82 1621 8081 6117 3.769 1.914 1.90522476716161e-37 5.15621983052412e-37 0.0182 0.0125 0.0159 0.0159 TRUE NA NA +CADAFUBG00000106 425 336 471 834 796 746 516 552 436 293 255 285 1005 1021 646 708 698 585 610.75 278 891 664 2.377 1.249 3.38815964666747e-14 6.22370667588616e-14 0.0177 0.0171 0.0174 0.0174 TRUE NA NA +CADAFUBG00000107 53144 48972 61579 2462 1890 4170 3773 3790 4100 36696 37127 37293 2968 2424 3610 5179 4792 5503 15065.66 37039 3001 5158 0.14 -2.84 6.77111165790674e-95 3.40965351956547e-94 0.0124 0.0121 0.0135 0.0135 TRUE NA NA +CADAFUBG00000108 7212 6474 7940 2590 2402 2687 2441 2803 2739 4980 4908 4809 3122 3081 2326 3350 3544 3676 3755.1 4899 2843 3523 0.72 -0.473 0.000121128851877274 0.000166487952655507 0.0084 0.0128 0.0107 0.0107 TRUE NA NA +CADAFUBG00000109 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA NA NA NA NA NA NA NA NA NA NA +CADAFUBG00000110 14442 12966 15756 4878 4453 5279 2908 3770 3183 9972 9830 9542 5880 5711 4570 3991 4767 4272 6503.92 9781 5387 4343 0.445 -1.168 1.15203893433919e-22 2.50397731163381e-22 0.0089 0.0124 0.0101 0.0101 TRUE NA NA +CADAFUBG00000111 1011 930 1224 805 790 1164 726 832 623 698 705 741 970 1013 1008 996 1052 836 891.14 715 997 961 1.344 0.427 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--- /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 +CADAFUBG00000001 151 131 183 31 35 44 19 31 18 104 99 111 37 45 38 26 39 24 58.24 105 40 30 0.751 -0.413 0.182492773171526 0.253967778820216 0 0.0658 0.0344 0.0344 TRUE NA NA +CADAFUBG00000002 142 134 153 650 629 783 136 241 151 98 102 93 783 807 678 187 305 203 361.6 98 756 232 0.308 -1.699 1.72494656533161e-18 2.26369375326981e-17 0.0264 0.0206 0.0236 0.0236 TRUE NA NA +CADAFUBG00000003 157 147 166 7 10 20 8 10 8 108 111 101 8 13 17 11 13 11 43.7 107 13 12 0.877 -0.19 0.668248395514016 0.739965504906111 0 0.0837 0.0483 0.0483 TRUE NA NA +CADAFUBG00000004 275 249 342 70 44 91 75 64 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0.0101 TRUE NA NA +CADAFUBG00000153 1067 1009 1246 446 460 863 1100 1117 1110 737 765 755 538 590 747 1510 1412 1490 949.21 752 625 1471 2.353 1.234 9.26417508714187e-23 1.7790198597924e-21 0.0069 0.0152 0.0101 0.0101 TRUE NA NA +CADAFUBG00000154 2255 1996 2479 840 943 1081 920 976 863 1557 1513 1501 1012 1209 936 1263 1234 1158 1264.94 1524 1052 1218 1.159 0.213 0.0660868578014481 0.105157214214241 0.0053 0.0144 0.0086 0.0086 TRUE NA NA +CADAFUBG00000155 2117 1869 2240 894 1119 993 582 716 449 1462 1417 1357 1078 1435 860 799 905 603 1101.61 1412 1124 769 0.685 -0.545 0.00387922685205162 0.00821280857941009 0.032 0.0148 0.0245 0.0245 TRUE NA NA +CADAFUBG00000156 26895 24837 31160 1776 1800 2159 1849 2462 1816 18571 18830 18871 2141 2309 1869 2538 3113 2437 7853.11 18757 2106 2696 1.281 0.357 0.00453156808904794 0.00944720092657788 0.0109 0.0123 0.011 0.011 TRUE NA NA +CADAFUBG00000157 471 438 508 2847 2505 3109 2469 3367 2107 325 332 308 3432 3213 2691 3389 4258 2828 2308.32 322 3112 3492 1.123 0.168 0.251938110261678 0.333129045670674 0.0164 0.0133 0.0151 0.0151 TRUE NA NA +CADAFUBG00000158 686 676 765 853 738 1342 1651 1995 1536 474 512 463 1028 947 1162 2266 2523 2061 1270.67 483 1046 2283 2.18 1.124 9.27965944239257e-19 1.25446274388378e-17 0.0082 0.0144 0.0109 0.0109 TRUE NA NA +CADAFUBG00000159 391 351 454 608 509 706 1156 1169 1113 270 266 275 733 653 611 1587 1478 1494 818.49 270 666 1520 2.286 1.193 5.53713664214913e-32 2.1054355423375e-30 6e-04 0.0158 0.0061 0.0061 TRUE NA NA +CADAFUBG00000160 167 132 152 2183 1935 3090 828 1006 883 115 100 92 2631 2482 2675 1136 1272 1185 1298.78 102 2596 1198 0.462 -1.115 1.46580511959655e-24 3.21601012906426e-23 0.0035 0.0143 0.0078 0.0078 TRUE NA NA +CADAFUBG00000161 1184 1105 1339 994 1022 1265 866 981 904 818 838 811 1198 1311 1095 1189 1240 1213 1079.17 822 1201 1214 1.012 0.018 0.862795028942814 0.901128885558132 0.0024 0.0148 0.0065 0.0065 TRUE NA NA +CADAFUBG00000162 2485 2264 2919 1151 1029 1998 1593 1603 1560 1716 1716 1768 1387 1320 1730 2186 2027 2094 1771.54 1733 1479 2102 1.422 0.508 1.55765700249457e-05 4.90312613186286e-05 0.0063 0.0137 0.0093 0.0093 TRUE NA NA +CADAFUBG00000163 1652 1438 1811 297 333 610 309 342 299 1141 1090 1097 358 427 528 424 432 401 655.41 1109 438 419 0.958 -0.061 0.679806577667918 0.750239821607609 0.0107 0.0167 0.0132 0.0132 TRUE NA NA +CADAFUBG00000164 9183 8076 9766 4375 3977 5624 1595 2200 1931 6341 6123 5914 5273 5101 4869 2189 2782 2592 4575.92 6126 5081 2521 0.497 -1.01 1.11241006043722e-19 1.64857789080944e-18 0.0077 0.0126 0.0086 0.0086 TRUE NA NA +CADAFUBG00000165 51 40 63 117 124 234 146 159 130 35 30 38 141 159 203 200 201 174 131.36 34 168 192 1.143 0.193 0.338163353360655 0.426290698796213 0.0116 0.0358 0.0227 0.0227 TRUE NA NA +CADAFUBG00000166 44 36 38 289 260 653 190 250 190 30 27 23 348 333 565 261 316 255 239.97 27 415 277 0.669 -0.58 0.0116486758393546 0.0221412428067786 0.0436 0.025 0.0348 0.0348 TRUE NA NA +CADAFUBG00000167 190 175 227 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2389.32 1611 2744 2813 1.025 0.036 0.635202440336725 0.71171308882058 0 0.0132 0.0038 0.0038 TRUE NA NA +CADAFUBG00007347 506 406 523 153 141 171 116 123 80 349 308 317 184 181 148 159 156 107 212.15 325 171 141 0.825 -0.278 0.110473386877112 0.164872244621604 0 0.0267 0.014 0.014 TRUE NA NA +CADAFUBG00007348 2536 2235 2668 927 1128 1289 628 691 586 1751 1694 1616 1117 1447 1116 862 874 786 1251.49 1687 1227 841 0.686 -0.543 3.1415471780474e-05 9.46430753386503e-05 0.0089 0.0144 0.0111 0.0111 TRUE NA NA +CADAFUBG00007349 392 360 471 852 708 1327 712 876 720 271 273 285 1027 908 1149 977 1108 966 773.76 276 1028 1017 0.989 -0.016 0.898648163417627 0.926809819716645 0.0065 0.016 0.01 0.01 TRUE NA NA +CADAFUBG00007350 499 425 551 617 640 766 981 1130 866 345 322 334 744 821 663 1346 1429 1162 796.19 334 743 1312 1.769 0.823 1.02287034152492e-11 6.82676541224742e-11 0.0055 0.0159 0.0093 0.0093 TRUE NA NA +CADAFUBG00007351 815 750 777 223 294 441 234 230 199 563 569 471 269 377 382 321 291 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0 2 0 0 4 2 6 0 0 0 2 0 0 5 3 8 2.05 0 1 5 5.225 2.385 0.0819218410470264 0.126966880635404 0.6521 1.5404 1.3013 1.3013 TRUE NA NA +CADAFUBG00010126 1 1 1 0 0 0 8 6 6 1 1 1 0 0 0 11 8 8 3.19 1 0 9 33.332 5.059 0.000432675619991915 0.00110118829792076 0 0.9971 0.5227 0.5227 TRUE NA NA +CADAFUBG00010127 0 1 0 0 0 0 0 1 2 0 1 0 0 0 0 0 1 3 0.52 0 0 1 4.872 2.285 0.174679876954069 NA 0 6.0138 4.7292 4.7292 TRUE NA NA +CADAFUBG00010128 0 0 0 4 3 1 4 9 7 0 0 0 5 4 1 5 11 9 3.98 0 3 8 2.686 1.426 0.139189405854265 0.201581743470881 0 0.801 0.5313 0.5313 TRUE NA NA +CADAFUBG00010129 0 0 1 0 2 0 3 1 2 0 0 1 0 3 0 4 1 3 1.25 0 1 3 2.58 1.367 0.355242020314738 NA 0 2.5259 1.8755 1.8755 TRUE NA NA +CADAFUBG00010130 12 3 8 0 1 3 1 5 3 8 2 5 0 1 3 1 6 4 3.45 5 1 4 2.486 1.314 0.234750281863611 0.314097391014482 0 0.923 0.6151 0.6151 TRUE NA NA +CADAFUBG00010131 6 6 9 4 1 3 5 9 10 4 5 5 5 1 3 7 11 13 6.06 5 3 10 3.39 1.761 0.0239322282689963 0.0424079440399741 0 0.5302 0.2471 0.2471 TRUE NA NA +CADAFUBG00010132 2 0 0 4 2 2 15 5 9 1 0 0 5 3 2 21 6 12 5.5 0 3 13 4.03 2.011 0.0197194478940412 0.0356241549689057 0 0.5828 0.3784 0.3784 TRUE NA NA +CADAFUBG00010133 0 0 0 2 0 1 9 9 8 0 0 0 2 0 1 12 11 11 4.19 0 1 11 8.934 3.159 0.00296873900627919 0.00642923645925315 0 0.7603 0.4829 0.4829 TRUE NA NA +CADAFUBG00010134 3 0 6 2 5 3 18 15 19 2 0 4 2 6 3 25 19 25 9.59 2 4 23 5.755 2.525 0.000580323787809215 0.00144422691808374 0 0.3393 0.2556 0.2556 TRUE NA NA +CADAFUBG00010135 2221 5341 1493 2705 11039 6246 2171 3753 2683 1534 4049 904 3260 14158 5407 2980 4746 3601 4515.41 2162 7608 3776 0.516 -0.955 0.218825018824974 0.295607357348273 0.4877 0.0126 0.1835 0.4877 TRUE NA NA +CADAFUBG00010136 0 0 0 2 0 2 2 0 0 0 0 0 2 0 2 3 0 0 0.77 0 1 1 0.728 -0.457 0.781879379220204 NA 0 4.1137 3.8261 3.8261 TRUE NA NA +CADAFUBG00010137 0 0 0 2 1 0 1 2 0 0 0 0 2 1 0 1 3 0 0.84 0 1 1 1.07 0.097 0.949995483512756 NA 0 3.7315 2.3364 2.3364 TRUE NA NA +CADAFUBG00010138 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA NA NA NA NA NA NA NA NA NA NA +CADAFUBG00010139 0 0 2 4 3 1 15 11 9 0 0 1 5 4 1 21 14 12 6.37 0 3 16 4.735 2.243 0.00634827562294378 0.0128228449831482 0 0.5047 0.3281 0.3281 TRUE NA NA +CADAFUBG00010140 69 69 99 1 5 8 7 6 8 48 52 60 1 6 7 10 8 11 22.49 53 5 10 1.819 0.863 0.137851273598917 0.199880025610789 0 0.1515 0.0829 0.0829 TRUE NA NA +CADAFUBG00010141 3381 9219 2626 3892 18792 10072 3331 6304 4273 2335 6989 1590 4691 24102 8719 4572 7971 5735 7411.56 3638 12504 6093 0.509 -0.973 0.236456511400358 0.315893189362404 0.5542 0.0123 0.2023 0.5542 TRUE NA NA +CADAFUBG00010142 0 0 0 4 1 0 10 11 12 0 0 0 5 1 0 14 14 16 5.54 0 2 15 6.736 2.752 0.00480849611454155 0.0099839520916847 0.1547 0.5787 0.4919 0.4919 TRUE NA NA +CADAFUBG00010143 167 190 286 30 18 59 19 28 15 115 144 173 36 23 51 26 35 20 69.39 144 37 27 0.736 -0.443 0.209399101879577 0.284930856620856 0.0463 0.0572 0.0529 0.0529 TRUE NA NA +CADAFUBG00010144 16 45 9 13 44 33 28 112 89 11 34 5 16 56 29 38 142 119 50.09 17 34 100 2.872 1.522 0.0157273456782638 0.0290388444870091 0.5139 0.0746 0.2844 0.2844 TRUE NA NA +CADAFUBG00010145 1 3 1 14 16 19 15 22 9 1 2 1 17 21 16 21 28 12 13.1 1 18 20 1.125 0.17 0.753004421024831 0.813064169505712 0 0.2515 0.1559 0.1559 TRUE NA NA +CADAFUBG00010146 55 49 75 11 4 12 3 6 8 38 37 45 13 5 10 4 8 11 19.09 40 9 8 0.782 -0.355 0.533165318737628 0.619570169491285 0 0.1764 0.1046 0.1046 TRUE NA NA +CADAFUBG00010147 43 43 39 182 278 258 147 190 204 30 33 24 219 357 223 202 240 274 177.89 29 266 239 0.898 -0.156 0.520601932373605 0.60822926215861 0.0454 0.0296 0.0379 0.0379 TRUE NA NA +CADAFUBG00010148 7 6 12 1 2 4 3 1 4 5 5 7 1 3 3 4 1 5 3.85 6 2 3 1.394 0.48 0.611823180355404 0.692099138711861 0 0.8276 0.3682 0.3682 TRUE NA NA +CADAFUBG00010149 20 21 35 36 15 54 11 8 8 14 16 21 43 19 47 15 10 11 21.81 17 36 12 0.333 -1.585 0.00149419462496963 0.00343628759053258 0.0818 0.1559 0.1178 0.1178 TRUE NA NA +CADAFUBG00010150 6 8 11 6 11 8 6 6 4 4 6 7 7 14 7 8 8 5 7.37 6 9 7 0.769 -0.379 0.576527664684459 0.65873114331137 0 0.4378 0.2086 0.2086 TRUE NA NA +CADAFUBG00010151 1315 1239 1602 215 574 394 130 367 175 908 939 970 259 736 341 178 464 235 559.03 939 445 292 0.664 -0.591 0.253627596119896 0.334895099248517 0.1994 0.0175 0.0996 0.1994 TRUE NA NA +CADAFUBG00010152 22 32 41 51 56 69 19 32 18 15 24 25 61 72 60 26 40 24 38.67 21 64 30 0.476 -1.071 0.00209906703625833 0.00467308042781653 0.0217 0.0931 0.0587 0.0587 TRUE NA NA +CADAFUBG00010153 2949 3176 4393 2624 3318 3622 2990 3598 3328 2036 2408 2660 3163 4255 3136 4104 4550 4466 3419.82 2368 3518 4373 1.242 0.313 0.0318532816374063 0.0548057905079153 0.0156 0.0128 0.015 0.015 TRUE NA NA +CADAFUBG00010154 27 35 48 31 13 22 10 11 9 19 27 29 37 17 19 14 14 12 20.78 25 24 13 0.554 -0.851 0.0850588326908734 0.131189641112103 0.0668 0.1629 0.1116 0.1116 TRUE NA NA +CADAFUBG00010155 234 223 380 10 7 14 5 4 2 162 169 230 12 9 12 7 5 3 67.61 187 11 5 0.456 -1.132 0.0416400039969682 0.0698071663704663 0.0591 0.0583 0.0587 0.0587 TRUE NA NA +CADAFUBG00010156 2 2 2 0 3 1 3 2 4 1 2 1 0 4 1 4 3 5 2.32 1 2 4 2.355 1.236 0.274938477672416 0.358080353562437 0 1.3677 0.6894 0.6894 TRUE NA NA +CADAFUBG00010157 8 7 11 1 2 0 1 1 1 6 5 7 1 3 0 1 1 1 2.8 6 1 1 1.126 0.171 0.887504125773436 0.918895996423322 0 1.1311 0.558 0.558 TRUE NA NA +CADAFUBG00010158 93 89 104 93 127 144 51 65 61 64 67 63 112 163 125 70 82 82 92.04 65 133 78 0.589 -0.763 0.000916937706582903 0.00219439655757954 0 0.046 0.0259 0.0259 TRUE NA NA +CADAFUBG00010159 45 46 50 7 10 6 1 0 2 31 35 30 8 13 5 1 0 3 14.08 32 9 1 0.189 -2.4 0.00508004191425278 0.0104716889912805 0 0.2348 0.1467 0.1467 TRUE NA NA +CADAFUBG00010160 5 2 3 21 23 29 18 17 20 3 2 2 25 29 25 25 21 27 17.75 2 26 24 0.916 -0.127 0.769587677439152 0.825738593983054 0 0.1888 0.091 0.091 TRUE NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_DESeq2_targetT048_tables.html Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,22 @@ +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8" /> + <title></title> + </head> + <body> + <h1>Galaxy Tool SARTools_DESeq2</h1> +<div>Run at 14/04/2015 14:26:02</div><br/> +<div><strong>Tables</strong> available for downloading</div><br/> +<div><table cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> +<tr><td><a href="T4vsT0.complete.txt">T4vsT0.complete.txt</a></td><td>1.9 MB</td></tr> +<tr><td><a href="T4vsT0.down.txt">T4vsT0.down.txt</a></td><td>850.5 KB</td></tr> +<tr><td><a href="T4vsT0.up.txt">T4vsT0.up.txt</a></td><td>822.0 KB</td></tr> +<tr><td><a href="T8vsT0.complete.txt">T8vsT0.complete.txt</a></td><td>1.9 MB</td></tr> +<tr><td><a href="T8vsT0.down.txt">T8vsT0.down.txt</a></td><td>836.9 KB</td></tr> +<tr><td><a href="T8vsT0.up.txt">T8vsT0.up.txt</a></td><td>824.5 KB</td></tr> +<tr><td><a href="T8vsT4.complete.txt">T8vsT4.complete.txt</a></td><td>1.9 MB</td></tr> +<tr><td><a href="T8vsT4.down.txt">T8vsT4.down.txt</a></td><td>515.3 KB</td></tr> +<tr><td><a href="T8vsT4.up.txt">T8vsT4.up.txt</a></td><td>594.5 KB</td></tr> +</table></div><br/> +</body></html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_DESeq2_target_tables.html Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,16 @@ +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8" /> + <title></title> + </head> + <body> + <h1>Galaxy Tool SARTools_DESeq2</h1> +<div>Run at 14/04/2015 14:15:36</div><br/> +<div><strong>Tables</strong> available for downloading</div><br/> +<div><table cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> +<tr><td><a href="KOvsWT.complete.txt">KOvsWT.complete.txt</a></td><td>1.2 MB</td></tr> +<tr><td><a href="KOvsWT.down.txt">KOvsWT.down.txt</a></td><td>395.7 KB</td></tr> +<tr><td><a href="KOvsWT.up.txt">KOvsWT.up.txt</a></td><td>407.9 KB</td></tr> +</table></div><br/> +</body></html> \ No newline at end of file
--- /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 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_T4vsT0_small.complete.txt Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,11 @@ +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 FC log2FoldChange pvalue padj tagwise.dispersion trended.dispersion +CADAFUBG00000001 151 131 183 31 35 44 19 31 18 134 67 134 29 33 49 39 63 34 64.49 112 37 45 0.329 -1.605 5.27496945728882e-05 0.000131874236432221 0.0936 0.0831 +CADAFUBG00000002 142 134 153 650 629 783 136 241 151 126 69 112 608 586 877 276 486 282 380.24 102 690 348 6.719 2.748 8.22681401828068e-11 2.74227133942689e-10 0.1097 0.109 +CADAFUBG00000003 157 147 166 7 10 20 8 10 8 139 76 121 7 9 22 16 20 15 47.28 112 13 17 0.109 -3.194 1.91402249895717e-12 9.57011249478584e-12 0.0984 0.0798 +CADAFUBG00000004 275 249 342 70 44 91 75 64 62 243 128 250 66 41 102 152 129 116 136.33 207 70 132 0.333 -1.585 0.000103946668101967 0.000207893336203933 0.1064 0.093 +CADAFUBG00000005 4 5 2 0 0 1 2 2 3 4 3 1 0 0 1 4 4 6 2.49 3 0 5 0.174 -2.52 0.0150859131969724 0.0215513045671034 0.0518 0.0534 +CADAFUBG00000006 2 0 1 0 1 2 7 3 3 2 0 1 0 1 2 14 6 6 3.5 1 1 9 1.361 0.445 0.671479929636785 0.671479929636785 0.0614 0.0537 +CADAFUBG00000007 4 7 3 0 0 0 0 0 0 4 4 2 0 0 0 0 0 0 1.04 3 0 0 0.037 -4.74 0.00020196975196529 0.000336616253275483 0.046 0.0519 +CADAFUBG00000008 10 16 10 28 12 10 16 33 23 9 8 7 26 11 11 32 67 43 23.88 8 16 47 1.941 0.957 0.0361184203960699 0.0401315782178554 0.0794 0.0697 +CADAFUBG00000009 12 20 24 74 84 77 10 10 9 11 10 18 69 78 86 20 20 17 36.61 13 78 19 6.123 2.614 2.33639483251369e-14 2.33639483251369e-13 0.0519 0.0761 +CADAFUBG00000010 269 262 379 112 132 138 44 33 48 238 135 277 105 123 155 89 67 90 141.97 217 128 82 0.586 -0.772 0.0278467472898115 0.0348084341122643 0.0822 0.0938
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_T8vsT0.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 FC log2FoldChange pvalue padj tagwise.dispersion trended.dispersion +CADAFUBG00000001 151 131 183 31 35 44 19 31 18 108 102 116 39 49 41 27 41 26 60.93 109 43 31 0.29 -1.784 3.0284161168739e-15 4.79568971962673e-15 0.0155 0.0215 +CADAFUBG00000002 142 134 153 650 629 783 136 241 151 101 104 97 823 883 736 195 317 215 385.58 101 814 242 2.411 1.269 2.91168180032616e-10 4.11901125794288e-10 0.0225 0.0213 +CADAFUBG00000003 157 147 166 7 10 20 8 10 8 112 114 105 9 14 19 11 13 11 45.41 110 14 12 0.11 -3.184 1.24075253440832e-31 2.68387296267432e-31 0.0154 0.0179 +CADAFUBG00000004 275 249 342 70 44 91 75 64 62 197 193 216 89 62 86 107 84 88 124.59 202 79 93 0.461 -1.117 2.37946669484576e-08 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_T8vsT0_small.complete.txt Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,11 @@ +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 FC log2FoldChange pvalue padj tagwise.dispersion trended.dispersion +CADAFUBG00000001 151 131 183 31 35 44 19 31 18 134 67 134 29 33 49 39 63 34 64.49 112 37 45 0.404 -1.308 0.00132454186292087 0.00220756977153478 0.0936 0.0831 +CADAFUBG00000002 142 134 153 650 629 783 136 241 151 126 69 112 608 586 877 276 486 282 380.24 102 690 348 3.406 1.768 1.7470045738652e-05 4.54620114688567e-05 0.1097 0.109 +CADAFUBG00000003 157 147 166 7 10 20 8 10 8 139 76 121 7 9 22 16 20 15 47.28 112 13 17 0.152 -2.714 5.3299888101895e-09 4.65534884508775e-08 0.0984 0.0798 +CADAFUBG00000004 275 249 342 70 44 91 75 64 62 243 128 250 66 41 102 152 129 116 136.33 207 70 132 0.642 -0.639 0.111835762044354 0.139794702555443 0.1064 0.093 +CADAFUBG00000005 4 5 2 0 0 1 2 2 3 4 3 1 0 0 1 4 4 6 2.49 3 0 5 1.81 0.856 0.245469236227214 0.245469236227214 0.0518 0.0534 +CADAFUBG00000006 2 0 1 0 1 2 7 3 3 2 0 1 0 1 2 14 6 6 3.5 1 1 9 10.528 3.396 1.81848045875427e-05 4.54620114688567e-05 0.0614 0.0537 +CADAFUBG00000007 4 7 3 0 0 0 0 0 0 4 4 2 0 0 0 0 0 0 1.04 3 0 0 0.038 -4.716 0.00492912024134794 0.00704160034478277 0.046 0.0519 +CADAFUBG00000008 10 16 10 28 12 10 16 33 23 9 8 7 26 11 11 32 67 43 23.88 8 16 47 5.812 2.539 9.31069769017549e-09 4.65534884508775e-08 0.0794 0.0697 +CADAFUBG00000009 12 20 24 74 84 77 10 10 9 11 10 18 69 78 86 20 20 17 36.61 13 78 19 1.508 0.593 0.165761916130055 0.184179906811172 0.0519 0.0761 +CADAFUBG00000010 269 262 379 112 132 138 44 33 48 238 135 277 105 123 155 89 67 90 141.97 217 128 82 0.38 -1.395 0.000153334659791212 0.000306669319582424 0.0822 0.0938
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_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 FC log2FoldChange pvalue padj tagwise.dispersion trended.dispersion +CADAFUBG00000001 151 131 183 31 35 44 19 31 18 108 102 116 39 49 41 27 41 26 60.93 109 43 31 0.732 -0.45 0.0889838918396072 0.131464254163587 0.0155 0.0215 +CADAFUBG00000002 142 134 153 650 629 783 136 241 151 101 104 97 823 883 736 195 317 215 385.58 101 814 242 0.299 -1.744 2.11601600580853e-19 3.53107602988708e-18 0.0225 0.0213 +CADAFUBG00000003 157 147 166 7 10 20 8 10 8 112 114 105 9 14 19 11 13 11 45.41 110 14 12 0.844 -0.244 0.534531983827705 0.606918730217373 0.0154 0.0179 +CADAFUBG00000004 275 249 342 70 44 91 75 64 62 197 193 216 89 62 86 107 84 88 124.59 202 79 93 1.175 0.233 0.288380044705298 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_T8vsT4_small.complete.txt Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,11 @@ +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 FC log2FoldChange pvalue padj tagwise.dispersion trended.dispersion +CADAFUBG00000001 151 131 183 31 35 44 19 31 18 134 67 134 29 33 49 39 63 34 64.49 112 37 45 1.229 0.297 0.483084442993157 0.536760492214619 0.0936 0.0831 +CADAFUBG00000002 142 134 153 650 629 783 136 241 151 126 69 112 608 586 877 276 486 282 380.24 102 690 348 0.507 -0.98 0.0143366822573135 0.0286733645146269 0.1097 0.109 +CADAFUBG00000003 157 147 166 7 10 20 8 10 8 139 76 121 7 9 22 16 20 15 47.28 112 13 17 1.395 0.48 0.357116799789164 0.446395999736455 0.0984 0.0798 +CADAFUBG00000004 275 249 342 70 44 91 75 64 62 243 128 250 66 41 102 152 129 116 136.33 207 70 132 1.926 0.945 0.0224556086120208 0.037426014353368 0.1064 0.093 +CADAFUBG00000005 4 5 2 0 0 1 2 2 3 4 3 1 0 0 1 4 4 6 2.49 3 0 5 10.386 3.377 0.00204407258531934 0.00511018146329835 0.0518 0.0534 +CADAFUBG00000006 2 0 1 0 1 2 7 3 3 2 0 1 0 1 2 14 6 6 3.5 1 1 9 7.734 2.951 0.000272141497083366 0.000907138323611221 0.0614 0.0537 +CADAFUBG00000007 4 7 3 0 0 0 0 0 0 4 4 2 0 0 0 0 0 0 1.04 3 0 0 1.017 0.024 0.999987137272799 0.999987137272799 0.046 0.0519 +CADAFUBG00000008 10 16 10 28 12 10 16 33 23 9 8 7 26 11 11 32 67 43 23.88 8 16 47 2.994 1.582 0.000223358535134501 0.000907138323611221 0.0794 0.0697 +CADAFUBG00000009 12 20 24 74 84 77 10 10 9 11 10 18 69 78 86 20 20 17 36.61 13 78 19 0.246 -2.021 7.39615350340289e-08 7.39615350340289e-07 0.0519 0.0761 +CADAFUBG00000010 269 262 379 112 132 138 44 33 48 238 135 277 105 123 155 89 67 90 141.97 217 128 82 0.649 -0.623 0.0917606977604112 0.131086711086302 0.0822 0.0938
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_targetT048_small_tables.html Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,22 @@ +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8" /> + <title></title> + </head> + <body> + <h1>Galaxy Tool SARTools_edgeR</h1> +<div>Run at 14/04/2015 15:27:39</div><br/> +<div><strong>Tables</strong> available for downloading</div><br/> +<div><table cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> +<tr><td><a href="T4vsT0.complete.txt">T4vsT0.complete.txt</a></td><td>1.7 KB</td></tr> +<tr><td><a href="T4vsT0.down.txt">T4vsT0.down.txt</a></td><td>1.1 KB</td></tr> +<tr><td><a href="T4vsT0.up.txt">T4vsT0.up.txt</a></td><td>697 B</td></tr> +<tr><td><a href="T8vsT0.complete.txt">T8vsT0.complete.txt</a></td><td>1.7 KB</td></tr> +<tr><td><a href="T8vsT0.down.txt">T8vsT0.down.txt</a></td><td>837 B</td></tr> +<tr><td><a href="T8vsT0.up.txt">T8vsT0.up.txt</a></td><td>680 B</td></tr> +<tr><td><a href="T8vsT4.complete.txt">T8vsT4.complete.txt</a></td><td>1.7 KB</td></tr> +<tr><td><a href="T8vsT4.down.txt">T8vsT4.down.txt</a></td><td>548 B</td></tr> +<tr><td><a href="T8vsT4.up.txt">T8vsT4.up.txt</a></td><td>798 B</td></tr> +</table></div><br/> +</body></html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_targetT048_tables.html Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,22 @@ +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8" /> + <title></title> + </head> + <body> + <h1>Galaxy Tool SARTools_edgeR</h1> +<div>Run at 14/04/2015 14:38:25</div><br/> +<div><strong>Tables</strong> available for downloading</div><br/> +<div><table cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> +<tr><td><a href="T4vsT0.complete.txt">T4vsT0.complete.txt</a></td><td>1.6 MB</td></tr> +<tr><td><a href="T4vsT0.down.txt">T4vsT0.down.txt</a></td><td>691.5 KB</td></tr> +<tr><td><a href="T4vsT0.up.txt">T4vsT0.up.txt</a></td><td>714.8 KB</td></tr> +<tr><td><a href="T8vsT0.complete.txt">T8vsT0.complete.txt</a></td><td>1.6 MB</td></tr> +<tr><td><a href="T8vsT0.down.txt">T8vsT0.down.txt</a></td><td>692.5 KB</td></tr> +<tr><td><a href="T8vsT0.up.txt">T8vsT0.up.txt</a></td><td>706.7 KB</td></tr> +<tr><td><a href="T8vsT4.complete.txt">T8vsT4.complete.txt</a></td><td>1.6 MB</td></tr> +<tr><td><a href="T8vsT4.down.txt">T8vsT4.down.txt</a></td><td>468.3 KB</td></tr> +<tr><td><a href="T8vsT4.up.txt">T8vsT4.up.txt</a></td><td>456.6 KB</td></tr> +</table></div><br/> +</body></html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_target_small_tables.html Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,16 @@ +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8" /> + <title></title> + </head> + <body> + <h1>Galaxy Tool SARTools_edgeR</h1> +<div>Run at 14/04/2015 14:36:39</div><br/> +<div><strong>Tables</strong> available for downloading</div><br/> +<div><table cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> +<tr><td><a href="KOvsWT.complete.txt">KOvsWT.complete.txt</a></td><td>1.4 KB</td></tr> +<tr><td><a href="KOvsWT.down.txt">KOvsWT.down.txt</a></td><td>799 B</td></tr> +<tr><td><a href="KOvsWT.up.txt">KOvsWT.up.txt</a></td><td>667 B</td></tr> +</table></div><br/> +</body></html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_target_tables.html Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,16 @@ +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8" /> + <title></title> + </head> + <body> + <h1>Galaxy Tool SARTools_edgeR</h1> +<div>Run at 14/04/2015 14:37:13</div><br/> +<div><strong>Tables</strong> available for downloading</div><br/> +<div><table cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> +<tr><td><a href="KOvsWT.complete.txt">KOvsWT.complete.txt</a></td><td>1.0 MB</td></tr> +<tr><td><a href="KOvsWT.down.txt">KOvsWT.down.txt</a></td><td>350.1 KB</td></tr> +<tr><td><a href="KOvsWT.up.txt">KOvsWT.up.txt</a></td><td>353.1 KB</td></tr> +</table></div><br/> +</body></html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group1_count1.txt Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,4502 @@ +gene0 1712 +gene1 1050 +gene10 49 +gene100 277 +gene1000 7 +gene1001 3 +gene1002 1 +gene1003 1 +gene1004 0 +gene1005 0 +gene1006 5 +gene1007 1 +gene1008 11 +gene1009 202 +gene101 67 +gene1010 279 +gene1011 30 +gene1012 55 +gene1013 10 +gene1014 23 +gene1015 6 +gene1016 75 +gene1017 136 +gene1018 3 +gene1019 183 +gene102 135 +gene1020 10 +gene1021 365 +gene1022 4 +gene1023 15 +gene1024 1 +gene1025 2 +gene1026 1 +gene1027 3 +gene1028 2 +gene1029 2 +gene103 6 +gene1030 24 +gene1031 288 +gene1032 1001 +gene1033 383 +gene1034 96 +gene1035 85 +gene1036 116 +gene1037 1 +gene1038 6 +gene1039 8 +gene104 9 +gene1040 2 +gene1041 14 +gene1042 1 +gene1043 0 +gene1044 5 +gene1045 64 +gene1046 5 +gene1047 199 +gene1048 126 +gene1049 106 +gene105 0 +gene1050 258 +gene1051 26 +gene1052 5 +gene1053 7 +gene1054 13 +gene1055 11 +gene1056 14 +gene1057 657 +gene1058 378 +gene1059 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/target.txt Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,6 @@ +label files group +WT1 WT1.htseq.out WT +WT2 WT2.htseq.out WT +KO1 KO1.htseq.out KO +KO2 KO2.htseq.out KO +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targetT048.txt Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,10 @@ +label files group batch +T0-1 sampleT0-1-htseq.out T0 1 +T0-5 sampleT0-5-htseq.out T0 2 +T0-6 sampleT0-6-htseq.out T0 3 +T4-1 sampleT4-1-htseq.out T4 1 +T4-2 sampleT4-2-htseq.out T4 2 +T4-3 sampleT4-3-htseq.out T4 3 +T8-1 sampleT8-1-htseq.out T8 1 +T8-2 sampleT8-2-htseq.out T8 2 +T8-3 sampleT8-3-htseq.out T8 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targetT048_small.txt Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,10 @@ +label files group batch +T0-1 sampleT0-1-htseq_small.out T0 1 +T0-5 sampleT0-5-htseq_small.out T0 2 +T0-6 sampleT0-6-htseq_small.out T0 3 +T4-1 sampleT4-1-htseq_small.out T4 1 +T4-2 sampleT4-2-htseq_small.out T4 2 +T4-3 sampleT4-3-htseq_small.out T4 3 +T8-1 sampleT8-1-htseq_small.out T8 1 +T8-2 sampleT8-2-htseq_small.out T8 2 +T8-3 sampleT8-3-htseq_small.out T8 3