| Next changeset 1:fe0ee346b17d (2017-04-26) |
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Commit message:
Planemo upload |
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added:
README.md abims_sartools_deseq2.xml abims_sartools_deseq2_wrapper.py abims_sartools_edger.xml abims_sartools_edger_wrapper.py macros.xml make_html.py pre_sartools.py pre_sartools.xml repository_dependencies.xml template_script_DESeq2_CL.r template_script_edgeR_CL.r test-data/SARTools_DESeq2_KOvsWT.complete.txt test-data/SARTools_DESeq2_T4vsT0.complete.txt test-data/SARTools_DESeq2_T8vsT0.complete.txt test-data/SARTools_DESeq2_T8vsT4.complete.txt test-data/SARTools_DESeq2_targetT048_tables.html test-data/SARTools_DESeq2_target_tables.html test-data/SARTools_edgeR_KOvsWT.complete.txt test-data/SARTools_edgeR_KOvsWT_small.complete.txt test-data/SARTools_edgeR_T4vsT0.complete.txt test-data/SARTools_edgeR_T4vsT0_small.complete.txt test-data/SARTools_edgeR_T8vsT0.complete.txt test-data/SARTools_edgeR_T8vsT0_small.complete.txt test-data/SARTools_edgeR_T8vsT4.complete.txt test-data/SARTools_edgeR_T8vsT4_small.complete.txt test-data/SARTools_edgeR_targetT048_small_tables.html test-data/SARTools_edgeR_targetT048_tables.html test-data/SARTools_edgeR_target_small_tables.html test-data/SARTools_edgeR_target_tables.html test-data/group1_count1.txt test-data/group1_count2.txt test-data/group2_count1.txt test-data/group2_count2.txt test-data/raw.zip test-data/rawT048.zip test-data/rawT048_small.zip test-data/raw_small.zip test-data/target.txt test-data/targetT048.txt test-data/targetT048_small.txt test-data/target_small.txt test-data/test_output_target.html |
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| diff -r 000000000000 -r 581d217c7337 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Jul 22 05:39:13 2016 -0400 |
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| @@ -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 + |
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| diff -r 000000000000 -r 581d217c7337 abims_sartools_deseq2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_sartools_deseq2.xml Fri Jul 22 05:39:13 2016 -0400 |
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| b'@@ -0,0 +1,194 @@\n+<tool id="sartools_deseq2" name="SARTools DESeq2" version="1.0.0">\n+ \n+ <!-- [REQUIRED] Tool description displayed after the tool name -->\n+ <description>Compare two or more biological conditions in a RNA-Seq framework with DESeq2</description>\n+ \n+ <macros>\n+ \t<import>macros.xml</import>\n+ </macros>\n+ \n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+ \n+ <!-- [REQUIRED] The command to execute -->\n+ <command interpreter="python"><![CDATA[\n+\t\n+\tabims_sartools_deseq2_wrapper.py\n+\t## parameters\n+\t@COMMAND_BASIC_PARAMETERS@\n+ \t#if str( $advanced_parameters.adv_param ) == "show":\n+ @COMMAND_BATCH_PARAM@\n+ --fitType $advanced_parameters.fitType\n+ --cooksCutoff $advanced_parameters.cooksCutoff\n+ --independentFiltering $advanced_parameters.independentFiltering\n+\t --alpha $advanced_parameters.alpha\n+\t --pAdjustMethod $advanced_parameters.pAdjustMethod\n+\t --typeTrans $advanced_parameters.typeTrans\n+\t --locfunc $advanced_parameters.locfunc\n+\t --colors $advanced_parameters.colors\n+ \t#end if\n+\t## ouputs\n+\t@COMMAND_OUTPUTS@\n+ \n+ ]]></command>\n+ \n+ <!-- [REQUIRED] Input files and tool parameters -->\n+ <inputs>\n+ \n+ <expand macro="basic_parameters" />\n+ \n+ <conditional name="advanced_parameters" >\n+ <param name="adv_param" type="select" label="Advanced Parameters" help="" >\n+ <option value="hide" selected="true">Hide</option>\n+ <option value="show">Show</option>\n+ </param>\n+ <when value="hide" />\n+ <when value="show">\n+\t\t<expand macro="batch_param" />\n+ <param name="fitType" type="select" label="Mean-variance relationship" help="(-f, --fitType) Type of model for the mean-dispersion relationship. Parametric by default." >\n+ \t\t<option value="parametric" selected="true">parametric</option>\n+\t\t\t<option value="local">local</option>\n+\t\t</param>\n+\t\t<param name="cooksCutoff" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" help="(-o, --cooksCutoff) Checked by default."/>\n+\t\t<param name="independentFiltering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" help="(-i, --independentFiltering) Checked by default."/>\n+\t\t<expand macro="alpha_param" />\n+\t\t<expand macro="padjustmethod_param" />\n+ \t<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." >\n+ \t<option value="VST" selected="true">VST</option>\n+ \t<option value="rlog">rlog</option>\n+ \t</param>\n+ \t<param name="locfunc" type="select" label="Estimation of the size factors" help="(-l --locfunc) \'median\' (default) or \'shorth\' from the genefilter package." >\n+ \t<option value="median" selected="true">median</option>\n+ \t<option value="shorth">shorth</option>\n+ \t</param>\n+\t\t<expand macro="colors_param" />\n+ </when>\n+ </conditional>\n+\n+ </inputs>\n+ \n+ <!-- [REQUIRED] Output files -->\n+ <outputs>\n+ \n+ <expand macro="outputs" /> \n+ \n+ </outputs>\n+ \n+ <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->\n+ <tests>\n+ <!-- [HELP] Test files have to be in the ~/test-data directory -->\n+ <test>\n+ <!-- Test with 2 conditions, 2 replicates, 8217 features -->\n+ <param name="targetFile" dbkey="?" value="target.txt" />\n+ <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/>\n+\t <param name="adv_param" value="show"/>\n+ <output name="log">\n+ <assert_contents>\n+ '..b' \t<extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_DESeq2_T4vsT0.complete.txt"/>\n+ \t<extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_DESeq2_T8vsT0.complete.txt"/>\n+ \t<extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_DESeq2_T8vsT4.complete.txt"/>\n+\t </output>\n+ </test>\n+--> </tests>\n+ \n+ <!-- [OPTIONAL] Help displayed in Galaxy -->\n+ <help><![CDATA[\n+\n+@HELP_AUTHORS@\n+\n+===============\n+SARTools DESeq2\n+===============\n+\n+-----------\n+Description\n+-----------\n+\n+@HELP_DESCRIPTION@\n+\n+\n+-----------\n+Input files\n+-----------\n+\n+@HELP_INPUT_FILES@\n+\n+\n+----------\n+Parameters\n+----------\n+\n+\t@HELP_BASIC_PARAMETERS@\n+\t* **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);\n+\t* **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);\n+\t* **fitType:** type of model for the mean-dispersion relationship ("parametric" by default, or "local");\n+\t* **cooksCutoff:** TRUE (default) of FALSE to execute or not the detection of the outliers [4];\n+\t* **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5];\n+\t* **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods);\n+\t* **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);\n+\t* **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package);\n+\t* **colors:** colors used for the figures (one per biological condition), 8 are given by default.\n+\n+\n+------------\n+Output files\n+------------\n+\n+@HELP_OUTPUT_FILES@\n+\n+\t\t\n+---------------------------------------------------\n+\n+[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\xe2\x80\x93420. Springer, New York, 2005.\n+\n+[2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011.\n+\n+[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.\n+\n+[4] R.-D. Cook. Detection of Influential Observation in Linear Regression. Technometrics, February 1977.\n+\n+[5] R. Bourgon, R. Gentleman, and W. Huber. Independent filtering increases detection power for high-throughput experiments. PNAS, 107(21):9546\xe2\x80\x939551, 2010. URL: http://www.pnas.org/content/107/21/9546.long.\n+\n+[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\xe2\x80\x93300, 1995.\n+\n+[7] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165\xe2\x80\x931188, 2001.\n+\n+\n+ ]]></help>\n+\n+ <citations>\n+ <expand macro="common_citations" /> \n+ <citation type="bibtex">@ARTICLE{Cook77,\n+ author = {R.-D. Cook},\n+ title = {Detection of Influential Observation in Linear Regression},\n+ journal = {Technometrics},\n+ year = {1977},\n+ month = {February}\n+ }</citation>\n+ <citation type="bibtex">@ARTICLE{Bourgon10,\n+ author = {R. Bourgon, R. Gentleman, and W. Huber},\n+ title = {Independent filtering increases detection power for high-throughput experiments},\n+ journal = {PNAS},\n+ year = {2010},\n+ volume = {107},\n+ number = {21},\n+ pages = {9546\xe2\x80\x939551},\n+ note = {URL: http://www.pnas.org/content/107/21/9546.long}\n+ }</citation>\n+ </citations>\n+ \n+</tool>\n' |
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| diff -r 000000000000 -r 581d217c7337 abims_sartools_deseq2_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_sartools_deseq2_wrapper.py Fri Jul 22 05:39:13 2016 -0400 |
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| @@ -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() + + |
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| diff -r 000000000000 -r 581d217c7337 abims_sartools_edger.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_sartools_edger.xml Fri Jul 22 05:39:13 2016 -0400 |
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| b'@@ -0,0 +1,190 @@\n+<tool id="sartools_edger" name="SARTools edgeR" version="1.0.0">\n+ \n+ <!-- [REQUIRED] Tool description displayed after the tool name -->\n+ <description>Compare two or more biological conditions in a RNA-Seq framework with edgeR</description>\n+ \n+ <macros>\n+ \t<import>macros.xml</import>\n+ </macros>\n+ \n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+\n+ \n+ <!-- [REQUIRED] The command to execute -->\n+ <command interpreter="python"><![CDATA[\n+\t\n+\tabims_sartools_edger_wrapper.py\n+\t## parameters\n+\t@COMMAND_BASIC_PARAMETERS@\n+ \t#if str( $advanced_parameters.adv_param ) == "show":\n+ @COMMAND_BATCH_PARAM@\n+\t --alpha $advanced_parameters.alpha\n+\t --pAdjustMethod $advanced_parameters.pAdjustMethod\n+\t --cpmCutoff $advanced_parameters.cpmCutoff\n+\t --geneSelection $advanced_parameters.geneSelection\n+\t --normalizationMethod $advanced_parameters.normalizationMethod\n+\t --colors $advanced_parameters.colors\n+ \t#end if\n+\t## ouputs\n+\t@COMMAND_OUTPUTS@\n+ \n+ ]]></command>\n+ \n+ <!-- [REQUIRED] Input files and tool parameters -->\n+ <inputs>\n+ \n+ <expand macro="basic_parameters" />\n+ \n+ <conditional name="advanced_parameters" >\n+ <param name="adv_param" type="select" label="Advanced Parameters" help="" >\n+ <option value="hide" selected="true">Hide</option>\n+ <option value="show">Show</option>\n+ </param>\n+ <when value="hide" />\n+ <when value="show">\n+\t\t<expand macro="batch_param" />\n+\t\t<expand macro="alpha_param" />\n+\t\t<expand macro="padjustmethod_param" />\n+\t\t<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." />\n+\t\t<param name="geneSelection" type="select" label="Selection of the features in MDSPlot" help="(-g, --gene.selection) Default is \'pairwise\'." >\n+ \t<option value="pairwise" selected="true">pairwise</option>\n+ \t<option value="common">common</option>\n+\t\t</param>\n+\t\t<param name="normalizationMethod" type="select" label="Normalization method in calcNormFactors" help="(-n, --normalizationMethod) \'TMM\' (default), \'RLE\' (DESeq method) or \'upperquartile\'." >\n+ \t<option value="TMM" selected="true">TMM</option>\n+ \t<option value="RLE">RLE</option>\n+ \t<option value="upperquartile">upperquartile</option>\n+\t\t</param>\n+\t\t<expand macro="colors_param" />\n+ </when>\n+ </conditional>\n+\n+ </inputs>\n+ \n+ <!-- [REQUIRED] Output files -->\n+ <outputs>\n+ \n+ <expand macro="outputs" /> \n+ \n+ </outputs>\n+ \n+ <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->\n+ <tests>\n+ <!-- [HELP] Test files have to be in the ~/test-data directory -->\n+ <test>\n+\t <!-- Test with 2 conditions, 2 replicates, 10 features -->\n+ <param name="targetFile" dbkey="?" value="target_small.txt" />\n+ <param name="rawDir" value="raw_small.zip" dbkey="?" ftype="zip"/>\n+\t <param name="adv_param" value="show"/>\n+ <output name="log">\n+ <assert_contents>\n+ <has_text text="KO vs WT 5 4 9" />\n+ <has_text text="HTML report created" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+<!-- <test>\n+--> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10 features, with batch effect -->\n+<!-- <param name="targetFile" dbkey="?" value="targetT048_small.txt" />\n+ <param name="rawDir" value="rawT048_small.zip" dbkey="?" ftype="no_unzip.zip"/>\n+\t <param name="condRef" value="T0"/>\n+\t <param name="adv_param" value="show"/>\n+\t <param name="condition" value="true"/>\n+ <output name="tables_html" file="SARTools_e'..b'pe="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4_small.complete.txt"/>\n+\t </output>\n+ </test>\n+--> <test>\n+ <!-- Test with 2 conditions, 2 replicates, 8217 features -->\n+ <param name="targetFile" dbkey="?" value="target.txt" />\n+ <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/>\n+\t <param name="adv_param" value="show"/>\n+ <output name="log">\n+ <assert_contents>\n+ <has_text text="KO vs WT 2691 2713 5404" />\n+ <has_text text="HTML report created" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+<!-- <test>\n+--> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect -->\n+<!-- <param name="targetFile" dbkey="?" value="targetT048.txt" />\n+ <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/>\n+\t <param name="condRef" value="T0"/>\n+\t <param name="adv_param" value="show"/>\n+\t <param name="condition" value="true"/>\n+ <output name="tables_html" file="SARTools_edgeR_targetT048_tables.html" lines_diff="14">\n+ \t<extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0.complete.txt"/>\n+ \t<extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0.complete.txt"/>\n+ \t<extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4.complete.txt"/>\n+\t </output>\n+ </test>\n+--> </tests>\n+ \n+ <!-- [OPTIONAL] Help displayed in Galaxy -->\n+ <help><![CDATA[\n+\n+@HELP_AUTHORS@\n+\n+==============\n+SARTools edgeR\n+==============\n+\n+-----------\n+Description\n+-----------\n+\n+@HELP_DESCRIPTION@\n+\n+\n+-----------\n+Input files\n+-----------\n+\n+@HELP_INPUT_FILES@\n+\n+\n+----------\n+Parameters\n+----------\n+\n+\t@HELP_BASIC_PARAMETERS@\n+\t* **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);\n+\t* **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);\n+\t* **pAdjustMethod:** p-value adjustment method for multiple testing [4, 5] ("BH" by default, "BY" or any value of p.adjust.methods);\n+\t* **cpmCutoff:** counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering);\n+\t* **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common);\n+\t* **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile";\n+\t* **colors:** colors used for the figures (one per biological condition), 8 are given by default.\n+\n+\n+------------\n+Output files\n+------------\n+\n+@HELP_OUTPUT_FILES@\n+\n+\t\t\n+---------------------------------------------------\n+\n+[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\xe2\x80\x93420. Springer, New York, 2005.\n+\n+[2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011.\n+\n+[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.\n+\n+[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\xe2\x80\x93300, 1995.\n+\n+[5] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165\xe2\x80\x931188, 2001.\n+\n+\n+ ]]></help>\n+\n+ <citations>\n+ <expand macro="common_citations" /> \n+ </citations>\n+ \n+</tool>\n' |
| b |
| diff -r 000000000000 -r 581d217c7337 abims_sartools_edger_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_sartools_edger_wrapper.py Fri Jul 22 05:39:13 2016 -0400 |
| b |
| @@ -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() + + |
| b |
| diff -r 000000000000 -r 581d217c7337 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jul 22 05:39:13 2016 -0400 |
| b |
| b'@@ -0,0 +1,261 @@\n+<macros>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="1.2.0">r-sartools</requirement>\n+ <requirement type="package" version="1.3.0">r-optparse</requirement>\n+ </requirements>\n+ </xml>\n+ \n+ <xml name="stdio">\n+ <stdio>\n+ <exit_code range="1" level="fatal" />\n+ <regex match="Execution halted"\n+ source="both"\n+ level="fatal"\n+ description="Execution halted" />\n+ <regex match="rsync error"\n+ source="both"\n+ level="fatal"\n+ description="rsync error" />\n+ </stdio>\n+ </xml>\n+\n+ <token name="@COMMAND_BASIC_PARAMETERS@">\n+\t--projectName $projectName\n+\t--author $author\n+\t--targetFile $targetFile\n+\t--rawDir $rawDir\n+\t--featuresToRemove $featuresToRemove\n+\t--varInt $varInt\n+\t--condRef $condRef\n+ </token>\n+\n+ <token name="@COMMAND_BATCH_PARAM@">\n+ #if $advanced_parameters.batch_condition.condition:\n+ --batch $advanced_parameters.batch_condition.batch\n+ #else:\n+ --batch NULL\n+ #end if\n+ </token>\n+\n+ <token name="@COMMAND_OUTPUTS@">\n+\t--figures_html $figures_html \n+\t--figures_html_files_path $figures_html.files_path\n+\t--tables_html $tables_html \n+\t--tables_html_files_path $tables_html.files_path\n+\t--rdata $rdata\n+\t--report_html $report_html\n+ \t--log $log\n+ </token>\n+\n+ <macro name="basic_parameters">\n+ <param name="projectName" type="text" value="Project" label="Name of the project used for the report" help="(-P, --projectName) No space allowed." >\n+\t\t<validator type="regex" message="Field requires a value. No space allowed.">\\S+</validator>\n+\t</param>\n+ <param name="author" type="text" value="Galaxy" label="Name of the report author" help="(-A, --author) No space allowed." >\n+\t\t<validator type="regex" message="Field requires a value. No space allowed.">\\S+</validator>\n+\t</param>\n+ <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." /> \n+ <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." /> \n+ <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\'." >\n+\t\t<validator type="regex" message="Field requires a value. No space allowed.">\\S+</validator>\n+\t</param>\n+ <param name="varInt" type="text" value="group" label="Factor of interest" help="(-v, --varInt) Biological condition in the target file. Default is \'group\'." >\n+\t\t<validator type="regex" message="Field requires a value. No space allowed.">\\S+</validator>\n+\t</param>\n+ <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\'." >\n+\t\t<validator type="regex" message="Field requires a value. No space allowed.">\\S+</validator>\n+\t</param>\n+ </macro>\n+\n+ <macro name="batch_param">\n+\t\t<conditional name="batch_condition">\n+\t\t\t<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."/>\n+ \t\t<when value="NULL" />\n+\t\t\t<when value="batch">\n+\t\t\t\t<param name="'..b'ct;\n+\t* **author:** author of the analysis;\n+\t* **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);\n+\t* **varInt:** variable of interest, i.e. biological condition, in the target file ("group" by default);\n+\t* **condRef:** reference biological condition used to compute fold-changes (no default, must be one of the levels of varInt);\n+ </token>\n+\n+ <token name="@HELP_OUTPUT_FILES@">\n+**Report:**\n+\n+\n+\t| 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. \n+\t| The user should read the full HTML report and closely analyze each figure to check that the analysis ran smoothly.\n+\n+\n+**Tables:**\n+\n+\n+\t* **TestVsRef.complete.txt:** contains all the features studied;\n+\t* **TestVsRef.down.txt:** contains only significant down-regulated features, i.e. less expressed in Test than in Ref;\n+\t* **TestVsRef.up.txt:** contains only significant up-regulated features i.e. more expressed in Test than in Ref.\n+\n+\n+**Figures:**\n+\n+\n+\t* **MAplot.png:** MA-plot for each comparison (log ratio of the means vs intensity).\n+\t* **PCA.png:** first and second factorial planes of the PCA on the samples based on VST or rlog data;\n+\t* **barplotNull.png:** percentage of null counts per sample;\n+\t* **barplotTC.png:** total number of reads per sample;\n+\t* **cluster.png:** hierachical clustering of the samples (based on VST or rlog data);\n+\t* **countsBoxplot.png:** boxplots on raw and normalized counts;\n+\t* **densplot.png:** estimation of the density of the counts for each sample;\n+\t* **diagSizeFactorsHist.png:** diagnostic of the estimation of the size factors;\n+\t* **diagSizeFactorsTC.png:** plot of the size factors vs the total number of reads;\n+\t* **dispersionsPlot.png:** graph of the estimations of the dispersions and diagnostic of log-linearity of the dispersions;\n+\t* **majSeq.png:** percentage of reads caught by the feature having the highest count in each sample;\n+\t* **pairwiseScatter.png:** pairwise scatter plot between each pair of samples and SERE values;\n+\t* **rawpHist.png:** histogram of the raw p-values for each comparison;\n+\t* **volcanoPlot.png:** vulcano plot for each comparison (\xe2\x88\x92 log10 (adjusted P value) vs log ratio of the means).\n+\n+\n+**R log file:**\n+\n+\n+\t| Give the R console outputs.\n+\n+\n+**R objects (.RData file):**\n+\n+\n+\t| Give all the R objects created during the analysis is saved: it may be used to perform downstream analyses.\n+ </token>\n+\n+ <macro name="common_citations">\n+ <citation type="doi">10.1371/journal.pone.0157022</citation>\n+ <citation type="bibtex">@INBOOK{Smyth05,\n+ author = {G.-K. Smyth},\n+ editor = {R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber},\n+ chapter = {Limma: linear models for microarray data},\n+ title = {Bioinformatics and Computational Biology Solutions Using R and Bioconductor},\n+ publisher = {Springer},\n+ year = {2005},\n+ pages = {397\xe2\x80\x93420}\n+ }</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu638</citation>\n+ <citation type="bibtex">@ARTICLE{Benjamini95,\n+ author = {Y. Benjamini and Y. Hochberg},\n+ title = {Controlling the false discovery rate: a practical and powerful approach to multiple testing},\n+ journal = {Journal of the Royal Statistical Society B},\n+ year = {1995},\n+ volume = {57},\n+ pages = {289\xe2\x80\x93300}\n+ }</citation>\n+ <citation type="bibtex">@ARTICLE{Benjamini01,\n+ author = {Y. Benjamini and D. Yekutieli},\n+ title = {The control of the false discovery rate in multiple testing under dependency},\n+ journal = {Ann. Statist.},\n+ year = {2001},\n+ volume = {29},\n+ number = {4},\n+ pages = {1165\xe2\x80\x931188}\n+ }</citation>\n+ </macro>\n+\n+</macros>\n' |
| b |
| diff -r 000000000000 -r 581d217c7337 make_html.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_html.py Fri Jul 22 05:39:13 2016 -0400 |
| b |
| @@ -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() |
| b |
| diff -r 000000000000 -r 581d217c7337 pre_sartools.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pre_sartools.py Fri Jul 22 05:39:13 2016 -0400 |
| [ |
| @@ -0,0 +1,74 @@ +#!/usr/bin/env python +#Author: Coline Billerey + +from os.path import basename, join +from os import getcwd, system +import argparse +from shutil import copyfile +import tempfile +import csv + +def __main__(): + + parser = argparse.ArgumentParser() + parser.add_argument('--batch') + parser.add_argument('--inputs', action='append' ,nargs='*') + parser.add_argument('--outfile') + parser.add_argument('--outarch') + args = parser.parse_args() + + batch=args.batch + outfile=args.outfile + outarch=args.outarch + inputs=args.inputs + counts_files = open( outfile, 'w' ) + + working_directory = getcwd() + file_zip=working_directory+"/counts.zip" + + + zip_cmd='zip -j %s' % (file_zip) + if batch and batch!="NULL": + counts_files.write("label\tfiles\tgroup\tbatch\n") + for (level, filename, label, batch_name ) in inputs: + filename_base = basename(filename) + # For RSEM files we process files as HTSeq count output + tmpdir = tempfile.mkdtemp() + with open(filename, 'rb') as csvfile: + with open(join(tmpdir, basename(filename)), 'wb') as out: + spamwriter = csv.writer(out, delimiter='\t') + reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True) + if len(reader.fieldnames) > 2: + for row in reader: + spamwriter.writerow((row['gene_id'], int(float(row['effective_length'])))) + zip_cmd += ' %s ' % (join(tmpdir, basename(filename))) + else : + zip_cmd += ' %s ' % (filename) + counts_files.write( label + "\t" + filename_base + "\t" + level + "\t" + batch_name + "\n" ) + else : + counts_files.write("label\tfiles\tgroup\n") + for (level, filename, label) in inputs: + filename_base = basename(filename) + # For RSEM files we process files as HTSeq count output + tmpdir = tempfile.mkdtemp() + with open(filename, 'rb') as csvfile: + with open(join(tmpdir, basename(filename)), 'wb') as out: + spamwriter = csv.writer(out, delimiter='\t') + reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True) + if len(reader.fieldnames) > 2: + for row in reader: + spamwriter.writerow((row['gene_id'], int(float(row['effective_length'])))) + zip_cmd += ' %s ' % (join(tmpdir, basename(filename))) + else: + zip_cmd += ' %s ' % (filename) + + counts_files.write( label + "\t" + filename_base + "\t" + level + "\n" ) + + counts_files.close() + system(zip_cmd) + copyfile(file_zip,outarch) + + + +if __name__=="__main__": + __main__() |
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| diff -r 000000000000 -r 581d217c7337 pre_sartools.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pre_sartools.xml Fri Jul 22 05:39:13 2016 -0400 |
| b |
| @@ -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> |
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| diff -r 000000000000 -r 581d217c7337 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Jul 22 05:39:13 2016 -0400 |
| b |
| @@ -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> |
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| diff -r 000000000000 -r 581d217c7337 template_script_DESeq2_CL.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_script_DESeq2_CL.r Fri Jul 22 05:39:13 2016 -0400 |
| [ |
| b'@@ -0,0 +1,192 @@\n+#!/local/gensoft2/exe/R/3.1.2/bin/Rscript\r\n+\r\n+# to run this script, use one of these commands:\r\n+# Rscript --no-save --no-restore --verbose template_script_DESeq2_CL.r -r raw -v group -c T0 > log.txt 2>&1\r\n+# Rscript template_script_DESeq2_CL.r -r raw -v group -c T0\r\n+\r\n+# to get help:\r\n+# Rscript template_script_DESeq2_CL.r --help\r\n+\r\n+################################################################################\r\n+### R script to compare several conditions with the SARTools and DESeq2 packages\r\n+### Hugo Varet\r\n+### April 20th, 2015\r\n+### designed to be executed with SARTools 1.1.0\r\n+################################################################################\r\n+\r\n+rm(list=ls()) # remove all the objects from the R session\r\n+library(optparse) # to run the script in command lines\r\n+\r\n+# options list with associated default value.\r\n+option_list <- list( \r\n+make_option(c("-P", "--projectName"),\r\n+\t\t\tdefault=basename(getwd()),\r\n+\t\t\tdest="projectName",\r\n+\t\t\thelp="name of the project used for the report [default: name of the current directory]."),\r\n+\r\n+make_option(c("-A", "--author"),\r\n+\t\t\tdefault=Sys.info()[7],\r\n+\t\t\tdest="author",\r\n+\t\t\thelp="name of the report author [default: %default]."),\r\n+\r\n+make_option(c("-t", "--targetFile"),\r\n+\t\t\tdefault="target.txt",\r\n+\t\t\tdest="targetFile",\r\n+\t\t\thelp="path to the design/target file [default: %default]."),\r\n+\r\n+make_option(c("-r", "--rawDir"),\r\n+\t\t\tdefault="raw",\r\n+\t\t\tdest="rawDir",\r\n+\t\t\thelp="path to the directory containing the HTSeq files [default: %default]."),\r\n+\r\n+make_option(c("-F", "--featuresToRemove"),\r\n+\t\t\tdefault="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual",\r\n+\t\t\tdest="FTR",\r\n+\t\t\thelp="names of the features to be removed, more than once can be specified [default: %default]"),\r\n+\t\t\t\r\n+make_option(c("-v", "--varInt"),\r\n+\t\t\tdefault="group",\r\n+\t\t\tdest="varInt", \r\n+\t\t\thelp="factor of interest [default: %default]"),\r\n+\r\n+make_option(c("-c", "--condRef"),\r\n+\t\t\tdefault="WT",\r\n+\t\t\tdest="condRef",\r\n+\t\t\thelp="reference biological condition [default: %default]"),\r\n+\r\n+make_option(c("-b", "--batch"),\r\n+\t\t\tdefault=NULL,\r\n+\t\t\tdest="batch",\r\n+\t\t\thelp="blocking factor [default: %default] or \\"batch\\" for example"),\r\n+\r\n+make_option(c("-f", "--fitType"),\r\n+\t\t\tdefault="parametric",\r\n+\t\t\tdest="fitType", \r\n+\t\t\thelp="mean-variance relationship: [default: %default] or local"),\r\n+\r\n+make_option(c("-o", "--cooksCutoff"),\r\n+\t\t\tdefault=TRUE,\r\n+\t\t\tdest="cooksCutoff", \r\n+\t\t\thelp="perform the outliers detection (default is TRUE)"),\r\n+\r\n+make_option(c("-i", "--independentFiltering"),\r\n+\t\t\tdefault=TRUE,\r\n+\t\t\tdest="independentFiltering",\r\n+\t\t\thelp="perform independent filtering (default is TRUE)"),\r\n+\r\n+make_option(c("-a", "--alpha"),\r\n+\t\t\tdefault=0.05,\r\n+\t\t\tdest="alpha", \r\n+\t\t\thelp="threshold of statistical significance [default: %default]"),\r\n+\r\n+make_option(c("-p", "--pAdjustMethod"),\r\n+\t\t\tdefault="BH",\r\n+\t\t\tdest="pAdjustMethod", \r\n+\t\t\thelp="p-value adjustment method: \\"BH\\" or \\"BY\\" [default: %default]"),\r\n+\r\n+make_option(c("-T", "--typeTrans"),\r\n+\t\t\tdefault="VST",\r\n+\t\t\tdest="typeTrans", \r\n+\t\t\thelp="transformation for PCA/clustering: \\"VST\\" ou \\"rlog\\" [default: %default]"),\r\n+\r\n+make_option(c("-l", "--locfunc"),\r\n+\t\t\tdefault="median",\r\n+\t\t\tdest="locfunc", \r\n+\t\t\thelp="median or shorth to estimate the size factors [default: %default]"),\r\n+\r\n+make_option(c("-C", "--colors"),\r\n+\t\t\tdefault="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",\r\n+\t\t\tdest="cols",\r\n+\t\t\thelp="colors of each biological condition on the plots\\n\\t\\t\\"col1,col2,col3,col4\\"\\n\\t\\t[default: %default]")\r\n+)\r\n+\r\n+# now parse the command line to check which option is given and get associated values\r\n+parser <- OptionParser(usage="usage: %prog [options]",\r\n+\t\t\t\t\t option_list=option_list, \r\n+\t\t\t\t\t description="Compare two or more biological conditions in a RNA-Seq framework with '..b'ng # TRUE/FALSE to perform independent filtering (default is TRUE)\r\n+alpha <- as.numeric(opt$alpha) # threshold of statistical significance\r\n+pAdjustMethod <- opt$pAdjustMethod # p-value adjustment method: "BH" (default) or "BY"\r\n+typeTrans <- opt$typeTrans # transformation for PCA/clustering: "VST" ou "rlog"\r\n+locfunc <- opt$locfunc # "median" (default) or "shorth" to estimate the size factors\r\n+colors <- unlist(strsplit(opt$cols, ",")) # vector of colors of each biologicial condition on the plots\r\n+\t\r\n+# print(paste("workDir", workDir))\r\n+# print(paste("projectName", projectName))\r\n+# print(paste("author", author))\r\n+# print(paste("targetFile", targetFile))\r\n+# print(paste("rawDir", rawDir))\r\n+# print(paste("varInt", varInt))\r\n+# print(paste("condRef", condRef))\r\n+# print(paste("batch", batch))\r\n+# print(paste("fitType", fitType))\r\n+# print(paste("cooksCutoff", cooksCutoff))\r\n+# print(paste("independentFiltering", independentFiltering))\r\n+# print(paste("alpha", alpha))\r\n+# print(paste("pAdjustMethod", pAdjustMethod))\r\n+# print(paste("typeTrans", typeTrans))\r\n+# print(paste("locfunc", locfunc))\r\n+# print(paste("featuresToRemove", featuresToRemove))\r\n+# print(paste("colors", colors))\r\n+\r\n+################################################################################\r\n+### running script ###\r\n+################################################################################\r\n+# setwd(workDir)\r\n+library(SARTools)\r\n+\r\n+# checking parameters\r\n+problem <- checkParameters.DESeq2(projectName=projectName,author=author,targetFile=targetFile,\r\n+ rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt,\r\n+ condRef=condRef,batch=batch,fitType=fitType,cooksCutoff=cooksCutoff,\r\n+ independentFiltering=independentFiltering,alpha=alpha,pAdjustMethod=pAdjustMethod,\r\n+ typeTrans=typeTrans,locfunc=locfunc,colors=colors)\r\n+if (problem) quit(save="yes")\r\n+\t\t\t\t\t \r\n+# loading target file\r\n+target <- loadTargetFile(targetFile=targetFile, varInt=varInt, condRef=condRef, batch=batch)\r\n+\r\n+# loading counts\r\n+counts <- loadCountData(target=target, rawDir=rawDir, featuresToRemove=featuresToRemove)\r\n+\r\n+# description plots\r\n+majSequences <- descriptionPlots(counts=counts, group=target[,varInt], col=colors)\r\n+\r\n+# analysis with DESeq2\r\n+out.DESeq2 <- run.DESeq2(counts=counts, target=target, varInt=varInt, batch=batch,\r\n+ locfunc=locfunc, fitType=fitType, pAdjustMethod=pAdjustMethod,\r\n+ cooksCutoff=cooksCutoff, independentFiltering=independentFiltering, alpha=alpha)\r\n+\r\n+# PCA + clustering\r\n+exploreCounts(object=out.DESeq2$dds, group=target[,varInt], typeTrans=typeTrans, col=colors)\r\n+\r\n+# summary of the analysis (boxplots, dispersions, diag size factors, export table, nDiffTotal, histograms, MA plot)\r\n+summaryResults <- summarizeResults.DESeq2(out.DESeq2, group=target[,varInt], col=colors,\r\n+ independentFiltering=independentFiltering, \r\n+ cooksCutoff=cooksCutoff, alpha=alpha)\r\n+\r\n+# save image of the R session\r\n+save.image(file=paste0(projectName, ".RData"))\r\n+\r\n+# generating HTML report\r\n+writeReport.DESeq2(target=target, counts=counts, out.DESeq2=out.DESeq2, summaryResults=summaryResults,\r\n+ majSequences=majSequences, workDir=workDir, projectName=projectName, author=author,\r\n+ targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt,\r\n+ condRef=condRef, batch=batch, fitType=fitType, cooksCutoff=cooksCutoff,\r\n+ independentFiltering=independentFiltering, alpha=alpha, pAdjustMethod=pAdjustMethod,\r\n+ typeTrans=typeTrans, locfunc=locfunc, colors=colors)\r\n' |
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| diff -r 000000000000 -r 581d217c7337 template_script_edgeR_CL.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_script_edgeR_CL.r Fri Jul 22 05:39:13 2016 -0400 |
| [ |
| b'@@ -0,0 +1,175 @@\n+#!/local/gensoft2/exe/R/3.1.2/bin/Rscript\r\n+\r\n+# to run this script, use one of these commands:\r\n+# Rscript --no-save --no-restore --verbose template_script_edgeR_CL.r -r raw -v group -c T0 > log.txt 2>&1\r\n+# Rscript template_script_edgeR_CL.r -r raw -v group -c T0\r\n+\r\n+# to get help:\r\n+# Rscript template_script_edgeR_CL.r --help\r\n+\r\n+################################################################################\r\n+### R script to compare several conditions with the SARTools and edgeR packages\r\n+### Hugo Varet\r\n+### April 20th, 2015\r\n+### designed to be executed with SARTools 1.1.0\r\n+################################################################################\r\n+\r\n+rm(list=ls()) # remove all the objects from the R session\r\n+library(optparse) # to run the script in command lines\r\n+\r\n+# options list with associated default value.\r\n+option_list <- list( \r\n+make_option(c("-P", "--projectName"),\r\n+\t\t\tdefault=basename(getwd()),\r\n+\t\t\tdest="projectName",\r\n+\t\t\thelp="name of the project used for the report [default: name of the current directory]."),\r\n+\r\n+make_option(c("-A", "--author"),\r\n+\t\t\tdefault=Sys.info()[7],\r\n+\t\t\tdest="author",\r\n+\t\t\thelp="name of the report author [default: %default]."),\r\n+\r\n+make_option(c("-t", "--targetFile"),\r\n+\t\t\tdefault="target.txt",\r\n+\t\t\tdest="targetFile",\r\n+\t\t\thelp="path to the design/target file [default: %default]."),\r\n+\r\n+make_option(c("-r", "--rawDir"),\r\n+\t\t\tdefault="raw",\r\n+\t\t\tdest="rawDir",\r\n+\t\t\thelp="path to the directory containing the HTSeq files [default: %default]."),\t\t\r\n+\r\n+make_option(c("-F", "--featuresToRemove"),\r\n+\t\t\tdefault="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual",\r\n+\t\t\tdest="FTR",\r\n+\t\t\thelp="names of the features to be removed, more than once can be specified [default: %default]"),\r\n+\t\t\t\r\n+make_option(c("-v", "--varInt"),\r\n+\t\t\tdefault="group",\r\n+\t\t\tdest="varInt", \r\n+\t\t\thelp="factor of interest [default: %default]"),\r\n+\r\n+make_option(c("-c", "--condRef"),\r\n+\t\t\tdefault="WT",\r\n+\t\t\tdest="condRef",\r\n+\t\t\thelp="reference biological condition [default: %default]"),\r\n+\r\n+make_option(c("-b", "--batch"),\r\n+\t\t\tdefault=NULL,\r\n+\t\t\tdest="batch",\r\n+\t\t\thelp="blocking factor [default: %default] or \\"batch\\" for example"),\r\n+\r\n+make_option(c("-a", "--alpha"),\r\n+\t\t\tdefault=0.05,\r\n+\t\t\tdest="alpha", \r\n+\t\t\thelp="threshold of statistical significance [default: %default]"),\r\n+\r\n+make_option(c("-p", "--pAdjustMethod"),\r\n+\t\t\tdefault="BH",\r\n+\t\t\tdest="pAdjustMethod", \r\n+\t\t\thelp="p-value adjustment method: \\"BH\\" or \\"BY\\" [default: %default]"),\r\n+\r\n+make_option(c("-m", "--cpmCutoff"),\r\n+\t\t\tdefault=1,\r\n+\t\t\tdest="cpmCutoff", \r\n+\t\t\thelp="counts-per-million cut-off to filter low counts"),\r\n+\t\t\t\r\n+make_option(c("-g", "--gene.selection"),\r\n+\t\t\tdefault="pairwise",\r\n+\t\t\tdest="gene.selection", \r\n+\t\t\thelp="selection of the features in MDSPlot [default: %default]"),\r\n+\t\t\t\r\n+make_option(c("-n", "--normalizationMethod"),\r\n+\t\t\tdefault="TMM",\r\n+\t\t\tdest="normalizationMethod", \r\n+\t\t\thelp="normalization method in calcNormFactors: \\"TMM\\", \\"RLE\\" or \\"upperquartile\\" [default: %default]"),\r\n+\r\n+make_option(c("-C", "--colors"),\r\n+\t\t\tdefault="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",\r\n+\t\t\tdest="cols",\r\n+\t\t\thelp="colors of each biological condition on the plots\\n\\t\\t\\"col1,col2,col3,col4\\"\\n\\t\\t[default: %default]")\r\n+)\r\n+\r\n+# now parse the command line to check which option is given and get associated values\r\n+parser <- OptionParser(usage="usage: %prog [options]",\r\n+\t\t\t\t\t option_list=option_list, \r\n+\t\t\t\t\t description="Compare two or more biological conditions in a RNA-Seq framework with edgeR.",\r\n+\t\t\t\t\t epilogue="For comments, bug reports etc... please contact Hugo Varet <hugo.varet@pasteur.fr>")\r\n+opt <- parse_args(parser, args=commandArgs(trailingOnly=TRUE), positional_arguments=0)$options\r\n+\r\n+# get options and arguments\r\n+workDir <- getwd()\r\n+projectName '..b'pt$FTR, ",")) # names of the features to be removed (specific HTSeq-count information and rRNA for example)\r\n+varInt <- opt$varInt # factor of interest\r\n+condRef <- opt$condRef # reference biological condition\r\n+batch <- opt$batch # blocking factor: NULL (default) or "batch" for example\r\n+alpha <- as.numeric(opt$alpha) # threshold of statistical significance\r\n+pAdjustMethod <- opt$pAdjustMethod # p-value adjustment method: "BH" (default) or "BY"\r\n+gene.selection <- opt$gene.selection # selection of the features in MDSPlot\r\n+normalizationMethod <- opt$normalizationMethod # normalization method in calcNormFactors\r\n+cpmCutoff <- opt$cpmCutoff # counts-per-million cut-off to filter low counts\r\n+colors <- unlist(strsplit(opt$cols, ",")) # vector of colors of each biologicial condition on the plots\r\n+\r\n+# print(paste("workDir", workDir))\r\n+# print(paste("projectName", projectName))\r\n+# print(paste("author", author))\r\n+# print(paste("targetFile", targetFile))\r\n+# print(paste("rawDir", rawDir))\r\n+# print(paste("varInt", varInt))\r\n+# print(paste("condRef", condRef))\r\n+# print(paste("batch", batch))\r\n+# print(paste("alpha", alpha))\r\n+# print(paste("pAdjustMethod", pAdjustMethod))\r\n+# print(paste("featuresToRemove", featuresToRemove))\r\n+# print(paste("colors", colors))\r\n+# print(paste("gene.selection", gene.selection))\r\n+# print(paste("normalizationMethod", normalizationMethod))\r\n+# print(paste("cpmCutoff", cpmCutoff))\r\n+\r\n+################################################################################\r\n+### running script ###\r\n+################################################################################\r\n+# setwd(workDir)\r\n+library(SARTools)\r\n+\r\n+# checking parameters\r\n+problem <- checkParameters.edgeR(projectName=projectName,author=author,targetFile=targetFile,\r\n+ rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt,\r\n+ condRef=condRef,batch=batch,alpha=alpha,pAdjustMethod=pAdjustMethod,\r\n+ cpmCutoff=cpmCutoff,gene.selection=gene.selection,\r\n+ normalizationMethod=normalizationMethod,colors=colors)\r\n+if (problem) quit(save="yes")\r\n+\t\t\t\t\t \r\n+# loading target file\r\n+target <- loadTargetFile(targetFile=targetFile, varInt=varInt, condRef=condRef, batch=batch)\r\n+\r\n+# loading counts\r\n+counts <- loadCountData(target=target, rawDir=rawDir, featuresToRemove=featuresToRemove)\r\n+\r\n+# description plots\r\n+majSequences <- descriptionPlots(counts=counts, group=target[,varInt], col=colors)\r\n+\r\n+# edgeR analysis\r\n+out.edgeR <- run.edgeR(counts=counts, target=target, varInt=varInt, condRef=condRef,\r\n+ batch=batch, cpmCutoff=cpmCutoff, normalizationMethod=normalizationMethod,\r\n+ pAdjustMethod=pAdjustMethod)\r\n+\r\n+# MDS + clustering\r\n+exploreCounts(object=out.edgeR$dge, group=target[,varInt], gene.selection=gene.selection, col=colors)\r\n+\r\n+# summary of the analysis (boxplots, dispersions, export table, nDiffTotal, histograms, MA plot)\r\n+summaryResults <- summarizeResults.edgeR(out.edgeR, group=target[,varInt], counts=counts, alpha=alpha, col=colors)\r\n+\r\n+# save image of the R session\r\n+save.image(file=paste0(projectName, ".RData"))\r\n+\r\n+# generating HTML report\r\n+writeReport.edgeR(target=target, counts=counts, out.edgeR=out.edgeR, summaryResults=summaryResults,\r\n+ majSequences=majSequences, workDir=workDir, projectName=projectName, author=author,\r\n+ targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt,\r\n+ condRef=condRef, batch=batch, alpha=alpha, pAdjustMethod=pAdjustMethod, colors=colors,\r\n+ gene.selection=gene.selection, normalizationMethod=normalizationMethod)\r\n' |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_KOvsWT.complete.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_DESeq2_KOvsWT.complete.txt Fri Jul 22 05:39:13 2016 -0400 |
| b |
| b'@@ -0,0 +1,8218 @@\n+Id\tWT1\tWT2\tKO1\tKO2\tnorm.WT1\tnorm.WT2\tnorm.KO1\tnorm.KO2\tbaseMean\tWT\tKO\tFoldChange\tlog2FoldChange\tpvalue\tpadj\tdispGeneEst\tdispFit\tdispMAP\tdispersion\tbetaConv\tmaxCooks\toutlier\n+feat0001\t2728\t1636\t668\t2378\t1106\t970\t2553\t2595\t1806.13\t1038\t2574\t2.451\t1.293\t5.37519651793256e-23\t6.36948912861346e-22\t0.0041\t0.0086\t0.0078\t0.0078\tTRUE\tNA\tNA\n+feat0002\t3169\t1892\t376\t1228\t1285\t1121\t1437\t1340\t1295.99\t1203\t1388\t1.147\t0.198\t0.160735832870222\t0.21103027167996\t0.0056\t0.0096\t0.0088\t0.0088\tTRUE\tNA\tNA\n+feat0003\t2784\t1626\t622\t2117\t1129\t964\t2377\t2311\t1695.16\t1046\t2344\t2.212\t1.145\t2.46807614980336e-17\t2.02427530084789e-16\t0.0062\t0.0088\t0.0083\t0.0083\tTRUE\tNA\tNA\n+feat0004\t6311\t4283\t374\t1470\t2560\t2539\t1429\t1604\t2032.99\t2550\t1516\t0.602\t-0.731\t1.04715254885587e-08\t4.04483408933959e-08\t5e-04\t0.0083\t0.0072\t0.0072\tTRUE\tNA\tNA\n+feat0005\t12769\t9132\t718\t3199\t5179\t5413\t2744\t3492\t4206.76\t5296\t3118\t0.596\t-0.746\t1.88312423678069e-08\t7.1167767069692e-08\t0.0144\t0.0072\t0.0083\t0.0083\tTRUE\tNA\tNA\n+feat0006\t3953\t2867\t666\t2579\t1603\t1699\t2545\t2815\t2165.68\t1651\t2680\t1.619\t0.695\t3.02564035998192e-08\t1.12082423279993e-07\t0.0024\t0.0082\t0.0072\t0.0072\tTRUE\tNA\tNA\n+feat0007\t4070\t2498\t310\t1039\t1651\t1481\t1185\t1134\t1362.51\t1566\t1160\t0.742\t-0.431\t0.0017821246875128\t0.00345101690390565\t0.0034\t0.0094\t0.0083\t0.0083\tTRUE\tNA\tNA\n+feat0008\t2750\t2026\t257\t924\t1115\t1201\t982\t1009\t1076.72\t1158\t996\t0.863\t-0.212\t0.134629764575021\t0.180478354843489\t0\t0.0103\t0.0086\t0.0086\tTRUE\tNA\tNA\n+feat0009\t2044\t1286\t118\t400\t829\t762\t451\t437\t619.69\t796\t444\t0.563\t-0.829\t7.71633809276032e-07\t2.40922220777453e-06\t0\t0.0133\t0.0113\t0.0113\tTRUE\tNA\tNA\n+feat0010\t3118\t2361\t511\t1885\t1265\t1399\t1953\t2057\t1668.57\t1332\t2005\t1.501\t0.586\t7.73270297819381e-06\t2.13511764456237e-05\t0.003\t0.0088\t0.0077\t0.0077\tTRUE\tNA\tNA\n+feat0011\t9296\t4990\t501\t1705\t3770\t2958\t1915\t1861\t2625.87\t3364\t1888\t0.565\t-0.823\t5.57421866989203e-09\t2.22471048700155e-08\t0.014\t0.0078\t0.0092\t0.0092\tTRUE\tNA\tNA\n+feat0012\t2933\t2233\t291\t1158\t1190\t1324\t1112\t1264\t1222.28\t1257\t1188\t0.953\t-0.07\t0.627334194643552\t0.684132682312554\t0.0056\t0.0098\t0.0091\t0.0091\tTRUE\tNA\tNA\n+feat0013\t1663\t1269\t149\t582\t674\t752\t569\t635\t657.82\t713\t602\t0.854\t-0.227\t0.169838645673078\t0.22147840244499\t0.0043\t0.0129\t0.0115\t0.0115\tTRUE\tNA\tNA\n+feat0014\t4406\t2749\t180\t589\t1787\t1629\t688\t643\t1186.78\t1708\t666\t0.393\t-1.347\t1.71373115477463e-20\t1.75205601922702e-19\t0.0029\t0.0099\t0.0086\t0.0086\tTRUE\tNA\tNA\n+feat0015\t1703\t1065\t121\t457\t691\t631\t462\t499\t570.79\t661\t480\t0.736\t-0.441\t0.00980452226009615\t0.0165938548810967\t0\t0.014\t0.012\t0.012\tTRUE\tNA\tNA\n+feat0016\t5355\t4114\t577\t2218\t2172\t2438\t2205\t2421\t2309.07\t2305\t2313\t1.007\t0.01\t0.938883543814683\t0.951058415401352\t0.0051\t0.0081\t0.0075\t0.0075\tTRUE\tNA\tNA\n+feat0017\t14929\t9447\t739\t2554\t6055\t5599\t2824\t2788\t4316.51\t5827\t2806\t0.485\t-1.045\t1.17780073804006e-19\t1.13220845140625e-18\t0.0017\t0.0072\t0.006\t0.006\tTRUE\tNA\tNA\n+feat0018\t3169\t2279\t444\t1522\t1285\t1351\t1697\t1661\t1498.53\t1318\t1679\t1.269\t0.344\t0.00818279452160768\t0.014077135924921\t0\t0.0091\t0.0074\t0.0074\tTRUE\tNA\tNA\n+feat0019\t5456\t4062\t445\t1567\t2213\t2408\t1701\t1710\t2007.85\t2310\t1706\t0.741\t-0.432\t0.000632633357501871\t0.0013176722739995\t0.002\t0.0084\t0.0071\t0.0071\tTRUE\tNA\tNA\n+feat0020\t9338\t6881\t650\t2420\t3787\t4078\t2484\t2641\t3247.79\t3932\t2562\t0.656\t-0.608\t3.28482909288193e-07\t1.07394290456432e-06\t0.0017\t0.0075\t0.0064\t0.0064\tTRUE\tNA\tNA\n+feat0021\t7675\t6038\t961\t3697\t3113\t3579\t3673\t4035\t3599.85\t3346\t3854\t1.153\t0.205\t0.100350704614807\t0.138518059586676\t0.0065\t0.0074\t0.0073\t0.0073\tTRUE\tNA\tNA\n+feat0022\t4253\t2845\t326\t1495\t1725\t1686\t1246\t1632\t1572.2\t1706\t1439\t0.855\t-0.226\t0.126779062818878\t0.171123022888893\t0.0168\t0.009\t0.0099\t0.0099\tTRUE\tNA\tNA\n+feat0023\t9504\t7828\t494\t1892\t3855\t4640\t1888\t2065\t3111.83\t4248\t1976\t0.472\t-1.084\t4.25038192544576e-16\t3.19911814519519e-15\t0.0098\t0.0076\t0.0081\t0.0081\tTRUE\tNA\tNA\n+feat0024\t3039\t2655\t268\t1079\t1233\t1574\t1024\t1178\t1252.03\t1404\t1101\t0.794\t-0.333\t0.0357410690108382\t0.0542897189468009\t0.018\t0.0097\t0.0113\t0.0113\tTRUE\tNA\tNA\n+feat0025\t3703\t2787\t477\t1955\t1502\t1652\t1823\t2134\t1777.63\t1577\t1978\t1.258\t0.3'..b'3\t8200\t842\t3091\t4381\t4860\t3218\t3374\t3958.32\t4620\t3296\t0.717\t-0.48\t4.89268216953205e-05\t0.000120904547715156\t0.0027\t0.0073\t0.0064\t0.0064\tTRUE\tNA\tNA\n+feat8191\t6333\t4023\t385\t1534\t2569\t2384\t1471\t1674\t2024.66\t2476\t1572\t0.643\t-0.638\t1.09592285345582e-06\t3.35532544859419e-06\t0.0045\t0.0083\t0.0076\t0.0076\tTRUE\tNA\tNA\n+feat8192\t7325\t5558\t1036\t3694\t2971\t3294\t3959\t4032\t3564.08\t31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|
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_T4vsT0.complete.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_DESeq2_T4vsT0.complete.txt Fri Jul 22 05:39:13 2016 -0400 |
| b |
| b'@@ -0,0 +1,10161 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|
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_T8vsT0.complete.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_DESeq2_T8vsT0.complete.txt Fri Jul 22 05:39:13 2016 -0400 |
| b |
| b'@@ -0,0 +1,10161 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|
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_T8vsT4.complete.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_DESeq2_T8vsT4.complete.txt Fri Jul 22 05:39:13 2016 -0400 |
| b |
| b'@@ -0,0 +1,10161 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|
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_targetT048_tables.html --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_DESeq2_target_tables.html --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_KOvsWT.complete.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_KOvsWT.complete.txt Fri Jul 22 05:39:13 2016 -0400 |
| b |
| b'@@ -0,0 +1,8218 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|
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_KOvsWT_small.complete.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_KOvsWT_small.complete.txt Fri Jul 22 05:39:13 2016 -0400 |
| b |
| @@ -0,0 +1,11 @@ +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 1493 1319 3258 3270 2335.02 1406 3264 2.319 1.214 1.58204812601667e-31 1.58204812601667e-30 0.0044 0.004 +feat0002 3169 1892 376 1228 1734 1525 1834 1689 1695.54 1630 1762 1.071 0.099 0.31282795266664 0.31282795266664 0.0036 0.004 +feat0003 2784 1626 622 2117 1523 1311 3034 2911 2194.85 1417 2972 2.09 1.063 6.31357155076041e-24 3.15678577538021e-23 0.0045 0.004 +feat0004 6311 4283 374 1470 3453 3453 1824 2021 2688.06 3453 1922 0.561 -0.833 7.25970877879939e-17 1.81492719469985e-16 0.0039 0.004 +feat0005 12769 9132 718 3199 6987 7363 3502 4399 5562.77 7175 3950 0.555 -0.851 6.51125384427663e-13 1.30225076885533e-12 0.0062 0.004 +feat0006 3953 2867 666 2579 2163 2312 3248 3547 2817.39 2238 3398 1.526 0.609 1.59875424853446e-09 2.6645904142241e-09 0.0043 0.004 +feat0007 4070 2498 310 1039 2227 2014 1512 1429 1795.49 2120 1470 0.688 -0.539 1.01634404978457e-08 1.45192007112082e-08 0.0032 0.004 +feat0008 2750 2026 257 924 1505 1633 1254 1271 1415.61 1569 1262 0.806 -0.31 0.00140423922365582 0.00156026580406202 0.0033 0.004 +feat0009 2044 1286 118 400 1118 1037 576 550 820.23 1078 563 0.518 -0.95 4.18036234386504e-18 1.39345411462168e-17 0.0033 0.004 +feat0010 3118 2361 511 1885 1706 1904 2492 2592 2173.58 1805 2542 1.414 0.499 4.0776526040795e-07 5.09706575509937e-07 0.0039 0.004 |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_T4vsT0.complete.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SARTools_edgeR_T4vsT0.complete.txt Fri Jul 22 05:39:13 2016 -0400 |
| b |
| b'@@ -0,0 +1,10161 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010129\t0\t0\t1\t0\t2\t0\t3\t1\t2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010130\t12\t3\t8\t0\t1\t3\t1\t5\t3\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010131\t6\t6\t9\t4\t1\t3\t5\t9\t10\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010132\t2\t0\t0\t4\t2\t2\t15\t5\t9\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010133\t0\t0\t0\t2\t0\t1\t9\t9\t8\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010134\t3\t0\t6\t2\t5\t3\t18\t15\t19\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010135\t2221\t5341\t1493\t2705\t11039\t6246\t2171\t3753\t2683\t1587\t4141\t943\t3425\t15488\t5873\t3110\t4931\t3822\t4813.32\t2224\t8262\t3954\t3.681\t1.88\t0.000152956270519319\t0.000185063520884559\t0.1642\t0.0141\n+CADAFUBG00010136\t0\t0\t0\t2\t0\t2\t2\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010137\t0\t0\t0\t2\t1\t0\t1\t2\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010138\t0\t0\t0\t0\t0\t0\t0\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010139\t0\t0\t2\t4\t3\t1\t15\t11\t9\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010140\t69\t69\t99\t1\t5\t8\t7\t6\t8\t49\t54\t63\t1\t7\t8\t10\t8\t11\t23.38\t55\t5\t10\t0.099\t-3.336\t1.76887817971899e-26\t3.4361978021033e-26\t0.0092\t0.0094\n+CADAFUBG00010141\t3381\t9219\t2626\t3892\t18792\t10072\t3331\t6304\t4273\t2416\t7149\t1658\t4928\t26366\t9470\t4771\t8282\t6088\t7903.06\t3741\t13588\t6380\t3.574\t1.838\t0.000480521558469965\t0.000571254983191434\t0.1854\t0.0151\n+CADAFUBG00010142\t0\t0\t0\t4\t1\t0\t10\t11\t12\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010143\t167\t190\t286\t30\t18\t59\t19\t28\t15\t119\t147\t181\t38\t25\t55\t27\t37\t21\t72.37\t149\t39\t28\t0.271\t-1.883\t1.17031100309784e-14\t1.81218968659872e-14\t0.0269\t0.0238\n+CADAFUBG00010144\t16\t45\t9\t13\t44\t33\t28\t112\t89\t11\t35\t6\t16\t62\t31\t40\t147\t127\t52.81\t17\t36\t105\t2\t1\t0.086167224934046\t0.0933116344610876\t0.2011\t0.0182\n+CADAFUBG00010145\t1\t3\t1\t14\t16\t19\t15\t22\t9\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010146\t55\t49\t75\t11\t4\t12\t3\t6\t8\t39\t38\t47\t14\t6\t11\t4\t8\t11\t19.9\t41\t10\t8\t0.252\t-1.988\t1.15414320040515e-12\t1.71782242194006e-12\t0.008\t0.0076\n+CADAFUBG00010147\t43\t43\t39\t182\t278\t258\t147\t190\t204\t31\t33\t25\t230\t390\t243\t211\t250\t291\t189.17\t30\t288\t251\t9.689\t3.276\t4.69950488294366e-34\t1.04658058989422e-33\t0.0355\t0.0284\n+CADAFUBG00010148\t7\t6\t12\t1\t2\t4\t3\t1\t4\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010149\t20\t21\t35\t36\t15\t54\t11\t8\t8\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010150\t6\t8\t11\t6\t11\t8\t6\t6\t4\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010151\t1315\t1239\t1602\t215\t574\t394\t130\t367\t175\t940\t961\t1012\t272\t805\t370\t186\t482\t249\t586.41\t971\t482\t306\t0.494\t-1.017\t0.0031327883848282\t0.00361579148256965\t0.0821\t0.0167\n+CADAFUBG00010152\t22\t32\t41\t51\t56\t69\t19\t32\t18\t16\t25\t26\t65\t79\t65\t27\t42\t26\t41.04\t22\t70\t32\t3.104\t1.634\t7.37963156934057e-12\t1.07803082962626e-11\t0.0176\t0.015\n+CADAFUBG00010153\t2949\t3176\t4393\t2624\t3318\t3622\t2990\t3598\t3328\t2107\t2463\t2774\t3322\t4655\t3405\t4283\t4727\t4741\t3608.71\t2448\t3794\t4584\t1.558\t0.639\t1.10010373451136e-05\t1.37617052320097e-05\t0.0148\t0.0136\n+CADAFUBG00010154\t27\t35\t48\t31\t13\t22\t10\t11\t9\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010155\t234\t223\t380\t10\t7\t14\t5\t4\t2\t167\t173\t240\t13\t10\t13\t7\t5\t3\t70.11\t193\t12\t5\t0.063\t-3.999\t5.44351363291324e-49\t1.53432457072012e-48\t0.021\t0.0238\n+CADAFUBG00010156\t2\t2\t2\t0\t3\t1\t3\t2\t4\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010157\t8\t7\t11\t1\t2\t0\t1\t1\t1\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010158\t93\t89\t104\t93\t127\t144\t51\t65\t61\t66\t69\t66\t118\t178\t135\t73\t85\t87\t97.54\t67\t144\t82\t2.131\t1.091\t6.36192241470246e-08\t8.48453774549239e-08\t0.0197\t0.0265\n+CADAFUBG00010159\t45\t46\t50\t7\t10\t6\t1\t0\t2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010160\t5\t2\t3\t21\t23\t29\t18\t17\t20\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n' |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_T4vsT0_small.complete.txt --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_T8vsT0.complete.txt --- /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 |
| b |
| b'@@ -0,0 +1,10161 @@\n+Id\tT0.1\tT0.5\tT0.6\tT4.1\tT4.2\tT4.3\tT8.1\tT8.2\tT8.3\tnorm.T0-1\tnorm.T0-5\tnorm.T0-6\tnorm.T4-1\tnorm.T4-2\tnorm.T4-3\tnorm.T8-1\tnorm.T8-2\tnorm.T8-3\tbaseMean\tT0\tT4\tT8\tFC\tlog2FoldChange\tpvalue\tpadj\ttagwise.dispersion\ttrended.dispersion\n+CADAFUBG00000001\t151\t131\t183\t31\t35\t44\t19\t31\t18\t108\t102\t116\t39\t49\t41\t27\t41\t26\t60.93\t109\t43\t31\t0.29\t-1.784\t3.0284161168739e-15\t4.79568971962673e-15\t0.0155\t0.0215\n+CADAFUBG00000002\t142\t134\t153\t650\t629\t783\t136\t241\t151\t101\t104\t97\t823\t883\t736\t195\t317\t215\t385.58\t101\t814\t242\t2.411\t1.269\t2.91168180032616e-10\t4.11901125794288e-10\t0.0225\t0.0213\n+CADAFUBG00000003\t157\t147\t166\t7\t10\t20\t8\t10\t8\t112\t114\t105\t9\t14\t19\t11\t13\t11\t45.41\t110\t14\t12\t0.11\t-3.184\t1.24075253440832e-31\t2.68387296267432e-31\t0.0154\t0.0179\n+CADAFUBG00000004\t275\t249\t342\t70\t44\t91\t75\t64\t62\t197\t193\t216\t89\t62\t86\t107\t84\t88\t124.59\t202\t79\t93\t0.461\t-1.117\t2.37946669484576e-08\t3.21224266030544e-08\t0.0198\t0.0284\n+CADAFUBG00000005\t4\t5\t2\t0\t0\t1\t2\t2\t3\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000006\t2\t0\t1\t0\t1\t2\t7\t3\t3\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000007\t4\t7\t3\t0\t0\t0\t0\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000008\t10\t16\t10\t28\t12\t10\t16\t33\t23\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000009\t12\t20\t24\t74\t84\t77\t10\t10\t9\t9\t16\t15\t94\t118\t72\t14\t13\t13\t40.39\t13\t95\t13\t1.024\t0.034\t0.92818180408743\t0.932695644762104\t0.0246\t0.0146\n+CADAFUBG00000010\t269\t262\t379\t112\t132\t138\t44\t33\t48\t192\t203\t239\t142\t185\t130\t63\t43\t68\t140.69\t211\t152\t58\t0.275\t-1.862\t2.2892515975556e-15\t3.63589507103914e-15\t0.0266\t0.0288\n+CADAFUBG00000011\t10065\t9593\t11955\t4076\t3739\t4137\t2736\t3311\t2749\t7192\t7439\t7549\t5161\t5246\t3890\t3919\t4350\t3916\t5406.87\t7393\t4766\t4062\t0.549\t-0.865\t3.43874369171954e-10\t4.857423288402e-10\t0.0133\t0.0144\n+CADAFUBG00000012\t651\t566\t819\t101\t86\t74\t97\t87\t96\t465\t439\t517\t128\t121\t70\t139\t114\t137\t236.6\t474\t106\t130\t0.273\t-1.871\t1.16918880583303e-17\t1.9484212909306e-17\t0.0274\t0.0265\n+CADAFUBG00000013\t118\t116\t150\t18\t24\t42\t15\t8\t5\t84\t90\t95\t23\t34\t39\t21\t11\t7\t44.9\t90\t32\t13\t0.146\t-2.774\t4.08564377827882e-23\t7.54448273109759e-23\t0.0173\t0.0175\n+CADAFUBG00000014\t288\t238\t304\t6\t6\t8\t2\t7\t3\t206\t185\t192\t8\t8\t8\t3\t9\t4\t69.13\t194\t8\t5\t0.029\t-5.098\t1.54296040545672e-60\t5.23911565566773e-60\t0.0182\t0.0236\n+CADAFUBG00000015\t18\t31\t39\t4\t4\t7\t2\t6\t2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000016\t1\t0\t0\t1\t1\t0\t2\t0\t1\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000017\t0\t0\t0\t0\t0\t0\t0\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000018\t1\t1\t2\t0\t0\t0\t0\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000019\t2\t3\t0\t0\t1\t0\t0\t0\t1\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000020\t0\t0\t0\t1\t1\t2\t0\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000021\t4\t1\t4\t1\t0\t0\t0\t2\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000022\t1\t0\t2\t0\t0\t0\t0\t1\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000023\t0\t1\t1\t0\t0\t0\t0\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000024\t7\t9\t5\t244\t181\t308\t159\t177\t173\t5\t7\t3\t309\t254\t290\t228\t233\t246\t174.93\t5\t284\t236\t46.618\t5.543\t1.57897565198041e-86\t7.73644056620278e-86\t0.0196\t0.0287\n+CADAFUBG00000025\t2\t1\t0\t35\t25\t38\t17\t29\t22\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000026\t602\t535\t669\t1453\t1042\t1911\t264\t733\t246\t430\t415\t422\t1840\t1462\t1797\t378\t963\t350\t895.29\t422\t1700\t564\t1.335\t0.417\t0.140293274860301\t0.150391829310702\t0.0555\t0.0139\n+CADAFUBG00000027\t20\t16\t18\t1\t1\t1\t1\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000028\t116\t118\t123\t86\t82\t78\t37\t55\t48\t83\t91\t78\t109\t115\t73\t53\t72\t68\t82.55\t84\t99\t64\t0.772\t-0.372\t0.101432629532381\t0.109718315695567\t0.0226\t0.0249\n+CADAFUBG00000029\t21\t23\t29\t2\t2\t1\t0\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00000030\t6\t6\t11\t3\t2\t2\t12\t11\t13\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t'..b'FUBG00010128\t0\t0\t0\t4\t3\t1\t4\t9\t7\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010129\t0\t0\t1\t0\t2\t0\t3\t1\t2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010130\t12\t3\t8\t0\t1\t3\t1\t5\t3\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010131\t6\t6\t9\t4\t1\t3\t5\t9\t10\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010132\t2\t0\t0\t4\t2\t2\t15\t5\t9\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010133\t0\t0\t0\t2\t0\t1\t9\t9\t8\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010134\t3\t0\t6\t2\t5\t3\t18\t15\t19\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010135\t2221\t5341\t1493\t2705\t11039\t6246\t2171\t3753\t2683\t1587\t4141\t943\t3425\t15488\t5873\t3110\t4931\t3822\t4813.32\t2224\t8262\t3954\t1.766\t0.82\t0.0893645661950405\t0.0969573389572249\t0.1642\t0.0141\n+CADAFUBG00010136\t0\t0\t0\t2\t0\t2\t2\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010137\t0\t0\t0\t2\t1\t0\t1\t2\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010138\t0\t0\t0\t0\t0\t0\t0\t0\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010139\t0\t0\t2\t4\t3\t1\t15\t11\t9\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010140\t69\t69\t99\t1\t5\t8\t7\t6\t8\t49\t54\t63\t1\t7\t8\t10\t8\t11\t23.38\t55\t5\t10\t0.178\t-2.489\t9.51593778155945e-18\t1.59012189956683e-17\t0.0092\t0.0094\n+CADAFUBG00010141\t3381\t9219\t2626\t3892\t18792\t10072\t3331\t6304\t4273\t2416\t7149\t1658\t4928\t26366\t9470\t4771\t8282\t6088\t7903.06\t3741\t13588\t6380\t1.686\t0.754\t0.140526779472975\t0.15060321022456\t0.1854\t0.0151\n+CADAFUBG00010142\t0\t0\t0\t4\t1\t0\t10\t11\t12\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010143\t167\t190\t286\t30\t18\t59\t19\t28\t15\t119\t147\t181\t38\t25\t55\t27\t37\t21\t72.37\t149\t39\t28\t0.195\t-2.358\t2.9405154005573e-19\t5.06733293611178e-19\t0.0269\t0.0238\n+CADAFUBG00010144\t16\t45\t9\t13\t44\t33\t28\t112\t89\t11\t35\t6\t16\t62\t31\t40\t147\t127\t52.81\t17\t36\t105\t5.607\t2.487\t2.75535861493651e-05\t3.42487010945391e-05\t0.2011\t0.0182\n+CADAFUBG00010145\t1\t3\t1\t14\t16\t19\t15\t22\t9\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010146\t55\t49\t75\t11\t4\t12\t3\t6\t8\t39\t38\t47\t14\t6\t11\t4\t8\t11\t19.9\t41\t10\t8\t0.191\t-2.388\t3.9539330611053e-14\t6.10603786651194e-14\t0.008\t0.0076\n+CADAFUBG00010147\t43\t43\t39\t182\t278\t258\t147\t190\t204\t31\t33\t25\t230\t390\t243\t211\t250\t291\t189.17\t30\t288\t251\t8.429\t3.075\t4.51456851027037e-30\t9.48379412790604e-30\t0.0355\t0.0284\n+CADAFUBG00010148\t7\t6\t12\t1\t2\t4\t3\t1\t4\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010149\t20\t21\t35\t36\t15\t54\t11\t8\t8\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010150\t6\t8\t11\t6\t11\t8\t6\t6\t4\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010151\t1315\t1239\t1602\t215\t574\t394\t130\t367\t175\t940\t961\t1012\t272\t805\t370\t186\t482\t249\t586.41\t971\t482\t306\t0.314\t-1.672\t1.95060038204467e-06\t2.50350353693129e-06\t0.0821\t0.0167\n+CADAFUBG00010152\t22\t32\t41\t51\t56\t69\t19\t32\t18\t16\t25\t26\t65\t79\t65\t27\t42\t26\t41.04\t22\t70\t32\t1.44\t0.526\t0.057835034466506\t0.0634134072729207\t0.0176\t0.015\n+CADAFUBG00010153\t2949\t3176\t4393\t2624\t3318\t3622\t2990\t3598\t3328\t2107\t2463\t2774\t3322\t4655\t3405\t4283\t4727\t4741\t3608.71\t2448\t3794\t4584\t1.88\t0.91\t4.36922416110639e-10\t6.16064190985206e-10\t0.0148\t0.0136\n+CADAFUBG00010154\t27\t35\t48\t31\t13\t22\t10\t11\t9\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010155\t234\t223\t380\t10\t7\t14\t5\t4\t2\t167\t173\t240\t13\t10\t13\t7\t5\t3\t70.11\t193\t12\t5\t0.027\t-5.204\t5.65028885999804e-57\t1.82551061890313e-56\t0.021\t0.0238\n+CADAFUBG00010156\t2\t2\t2\t0\t3\t1\t3\t2\t4\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010157\t8\t7\t11\t1\t2\t0\t1\t1\t1\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010158\t93\t89\t104\t93\t127\t144\t51\t65\t61\t66\t69\t66\t118\t178\t135\t73\t85\t87\t97.54\t67\t144\t82\t1.22\t0.286\t0.183937109899731\t0.195323801121746\t0.0197\t0.0265\n+CADAFUBG00010159\t45\t46\t50\t7\t10\t6\t1\t0\t2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+CADAFUBG00010160\t5\t2\t3\t21\t23\t29\t18\t17\t20\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n' |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_T8vsT0_small.complete.txt --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_T8vsT4.complete.txt --- /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 |
| b |
| b'@@ -0,0 +1,10161 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|
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| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_T8vsT4_small.complete.txt --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_targetT048_small_tables.html --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_targetT048_tables.html --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_target_small_tables.html --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/SARTools_edgeR_target_tables.html --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/group1_count1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group1_count1.txt Fri Jul 22 05:39:13 2016 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 581d217c7337 test-data/group1_count2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group1_count2.txt Fri Jul 22 05:39:13 2016 -0400 |
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|
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/group2_count1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group2_count1.txt Fri Jul 22 05:39:13 2016 -0400 |
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|
| b |
| diff -r 000000000000 -r 581d217c7337 test-data/group2_count2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group2_count2.txt Fri Jul 22 05:39:13 2016 -0400 |
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