Mercurial > repos > joachim-jacob > vstranformation
changeset 0:a48dde9abecf draft
Uploaded initial version
| author | joachim-jacob |
|---|---|
| date | Wed, 17 Jul 2013 04:06:12 -0400 |
| parents | |
| children | 7d7d6c743df0 |
| files | README test-data/counttable1.tsv test-data/vst_transf_htmlout.html test-data/vst_transf_tabout.txt tool_dependencies.xml vst_transformation.pl vst_transformation.xml |
| diffstat | 7 files changed, 32064 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Wed Jul 17 04:06:12 2013 -0400 @@ -0,0 +1,28 @@ +VSTransformation - 1.0.0 +============================= +<joachim.jacob@vib.be> + +SUMMARY +------- +This tool takes in a count table generated from a mapping of RNA-seq data, +and performs a variance stabilizing transformation on these counts. + +REQUIREMENTS AND INSTALLATION +----------------------------- +Install this tool in your Galaxy via the Toolshed + + ) Third party code installation + You need to have a working R environment available in your path, + with following dependencies installed: + - reshape + - ggplot2 + - deseq + - knitr + - markdown + + ) Integration into Galaxy + Just use the Management interface to integrate this tool. + +DETAILS AND ISSUES +------------------ + ) Soon dependencies will be resolved.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counttable1.tsv Wed Jul 17 04:06:12 2013 -0400 @@ -0,0 +1,15683 @@ +GeneID can_1 can_2 nbg_1 nbg_2 n18_1 n18_2 n25_1 n25_2 +FBgn0000003 33 41 150 1817 35 58 168 68 +FBgn0000008 798 711 630 777 679 721 626 792 +FBgn0000014 0 3 1 1 3 3 3 5 +FBgn0000015 0 0 1 0 2 0 1 0 +FBgn0000017 4335 3393 3201 4123 3603 3891 3254 4085 +FBgn0000018 165 142 138 135 116 147 112 174 +FBgn0000022 0 0 0 0 0 0 0 0 +FBgn0000024 7241 5601 4691 6767 5270 6021 5116 6197 +FBgn0000028 356 307 293 378 381 442 336 413 +FBgn0000032 318 295 267 304 320 342 277 331 +FBgn0000036 845 588 421 761 708 760 597 766 +FBgn0000037 3167 2600 2629 3092 2138 2397 2126 2751 +FBgn0000038 16133 12965 13243 14216 11525 13016 10897 14021 +FBgn0000039 1775 1433 1594 1531 1653 1776 1280 1695 +FBgn0000042 17647 14551 17832 19160 16484 18013 17594 23033 +FBgn0000043 634 503 571 611 352 337 429 587 +FBgn0000044 23888 16727 21338 19082 12992 13742 15033 12925 +FBgn0000045 1834 1616 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+hljs.initHighlightingOnLoad(); +</script> + +<!-- MathJax scripts --> +<script type="text/javascript" src="https://c328740.ssl.cf1.rackcdn.com/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> +</script> + + +<style type="text/css"> +body, td { + font-family: sans-serif; + background-color: white; + font-size: 12px; + margin: 8px; +} + +tt, code, pre { + font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace; +} + +h1 { + font-size:2.2em; +} + +h2 { + font-size:1.8em; +} + +h3 { + font-size:1.4em; +} + +h4 { + font-size:1.0em; +} + +h5 { + font-size:0.9em; +} + +h6 { + font-size:0.8em; +} + +a:visited { + color: rgb(50%, 0%, 50%); +} + +pre { + margin-top: 0; + max-width: 95%; + border: 1px solid #ccc; + white-space: pre-wrap; +} + +pre code { + display: block; padding: 0.5em; +} + +code.r, code.cpp { + background-color: #F8F8F8; +} + +table, td, th { + border: none; +} + +blockquote { + color:#666666; + margin:0; + padding-left: 1em; + border-left: 0.5em #EEE solid; +} + +hr { + height: 0px; + border-bottom: none; + border-top-width: thin; + border-top-style: dotted; + border-top-color: #999999; +} + +@media print { + * { + background: transparent !important; + color: black !important; + filter:none !important; + -ms-filter: none !important; + } + + body { + font-size:12pt; + max-width:100%; + } + + a, a:visited { + text-decoration: underline; + } + + hr { + visibility: hidden; + page-break-before: always; + } + + pre, blockquote { + padding-right: 1em; + page-break-inside: avoid; + } + + tr, img { + page-break-inside: avoid; + } + + img { + max-width: 100% !important; + } + + @page :left { + margin: 15mm 20mm 15mm 10mm; + } + + @page :right { + margin: 15mm 10mm 15mm 20mm; + } + + p, h2, h3 { + orphans: 3; widows: 3; + } + + h2, h3 { + page-break-after: avoid; + } +} +</style> + + + +</head> + +<body> +<h1>VST transformation</h1> + +<hr/> + +<p>Loading the R environment</p> + +<pre><code class="r">library("DESeq") +library(reshape) +library(ggplot2) +</code></pre> + +<p>Reading input</p> + +<pre><code class="r">filename = "counttable1.tsv" +raw_counts = read.csv(filename, sep = "\t", header = T, row.names = 1, stringsAsFactors = F) +raw_counts_deseqct = newCountDataSet(raw_counts[, c(1, 2)], factor(c("can", + "can"))) +</code></pre> + +<hr/> + +<p>Performing VST transformation</p> + +<pre><code class="r">raw_counts_deseqct = newCountDataSet(raw_counts[, c(1, 2)], factor(c("can", + "can"))) +raw_counts_deseqct = estimateSizeFactors(raw_counts_deseqct) +raw_counts_deseqctBlind = estimateDispersions(raw_counts_deseqct, method = "blind") +vsd = varianceStabilizingTransformation(raw_counts_deseqctBlind) +vst_raw_counts = exprs(vsd) +</code></pre> + +<hr/> + +<pre><code class="r">write.table(vst_raw_counts, file = "vst_transf_tabout.txt", sep = "\t", quote = F, + col.names = NA, row.names = TRUE) +head(vst_raw_counts) +</code></pre> + +<pre><code>## can_1 can_2 +## FBgn0000003 10.095 10.155 +## FBgn0000008 11.078 11.130 +## FBgn0000014 9.834 9.921 +## FBgn0000015 9.834 9.834 +## FBgn0000017 12.450 12.406 +## FBgn0000018 10.414 10.429 +</code></pre> + +<pre><code class="r">vst_raw_counts_melted = melt(vst_raw_counts) +ggplot(data = vst_raw_counts_melted, aes(value, colour = X2)) +</code></pre> + +<pre><code>## Error: No layers in plot +</code></pre> + +<pre><code class="r">+geom_density(alpha = 0.2) +</code></pre> + +<pre><code>## Error: invalid argument to unary operator +</code></pre> + +<pre><code class="r">+labs(x = "VST of counts") +</code></pre> + +<pre><code>## Error: invalid argument to unary operator +</code></pre> + +<pre><code class="r"> +for (sample in colnames(vst_raw_counts)) { + hist(vst_raw_counts[, colnames(vst_raw_counts) == sample], main = paste("Sample", + sample), breaks = 80, xlab = "VST counts") +} +</code></pre> + +<p><img 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alt="plot of chunk plotting and writing"/> <img 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alt="plot of chunk plotting and writing"/> </p> + +<hr/> + +<hr/> + +<p>Logging R environment</p> + +<pre><code class="r">sessionInfo() +</code></pre> + +<pre><code>## R version 3.0.1 (2013-05-16) +## Platform: x86_64-pc-linux-gnu (64-bit) +## +## locale: +## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C +## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 +## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 +## [7] LC_PAPER=C LC_NAME=C +## [9] LC_ADDRESS=C LC_TELEPHONE=C +## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C +## +## attached base packages: +## [1] parallel stats graphics grDevices utils datasets methods +## [8] base +## +## other attached packages: +## [1] ggplot2_0.9.3.1 reshape_0.8.4 plyr_1.8 +## [4] DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 +## [7] Biobase_2.20.1 BiocGenerics_0.6.0 markdown_0.6.1 +## [10] knitr_1.2 +## +## loaded via a namespace (and not attached): +## [1] annotate_1.38.0 AnnotationDbi_1.22.6 colorspace_1.2-2 +## [4] DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 +## [7] evaluate_0.4.4 formatR_0.8 genefilter_1.42.0 +## [10] geneplotter_1.38.0 grid_3.0.1 gtable_0.1.2 +## [13] IRanges_1.18.2 labeling_0.2 MASS_7.3-27 +## [16] munsell_0.4.2 proto_0.3-10 RColorBrewer_1.0-5 +## [19] reshape2_1.2.2 RSQLite_0.11.4 scales_0.2.3 +## [22] splines_3.0.1 stats4_3.0.1 stringr_0.6.2 +## [25] survival_2.37-4 tools_3.0.1 XML_3.98-1.1 +## [28] xtable_1.7-1 +</code></pre> + +<hr/> + +</body> + +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vst_transf_tabout.txt Wed Jul 17 04:06:12 2013 -0400 @@ -0,0 +1,15683 @@ + can_1 can_2 +FBgn0000003 10.0947087365926 10.155217055649 +FBgn0000008 11.0778113307378 11.1295635190438 +FBgn0000014 9.83428318137882 9.92126201825076 +FBgn0000015 9.83428318137882 9.83428318137882 +FBgn0000017 12.4499264643294 12.4057034332022 +FBgn0000018 10.413505307596 10.4285708023499 +FBgn0000022 9.83428318137882 9.83428318137882 +FBgn0000024 13.0136340448334 12.9507956467019 +FBgn0000028 10.6787049368095 10.7011923487049 +FBgn0000032 10.6335464215559 10.684563679743 +FBgn0000036 11.1117454091996 11.0186332794786 +FBgn0000037 12.1367362187378 12.1414311086754 +FBgn0000038 13.9975905167321 13.9764048635141 +FBgn0000039 11.6288830936994 11.6194562026446 +FBgn0000042 14.1138264268777 14.1258994844848 +FBgn0000043 10.949357728479 10.9338982360254 +FBgn0000044 14.5130699691432 14.3085550828035 +FBgn0000045 11.6550947744403 11.716859269806 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jul 17 04:06:12 2013 -0400 @@ -0,0 +1,51 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="package_r3" version="3.0.1"> + <repository changeset_revision="6344ee60d0cf" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="r_additions" version="1.0.0"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="6344ee60d0cf" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <package name="r3" version="3.0.1" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR</action> + <action type="shell_command">echo "install.packages('reshape')" > $INSTALL_DIR/runme.R </action> + <action type="shell_command">echo "install.packages('knitr')" >> $INSTALL_DIR/runme.R </action> + <action type="shell_command">echo "install.packages('markdown')" >> $INSTALL_DIR/runme.R </action> + <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && + R CMD BATCH $INSTALL_DIR/runme.R > $INSTALL_DIR/install.log </action> + <action type="shell_command">cat $INSTALL_DIR/install.log</action> + </actions> + </install> + <readme>Installs knitr, reshape and markdown packages for R3.0 </readme> + <package name="biocbasics" version="2.12"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="6344ee60d0cf" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <package name="r3" version="3.0.1" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR</action> + <action type="shell_command">echo "install.packages('reshape')" > $INSTALL_DIR/runme.R </action> + <action type="shell_command">echo "install.packages('knitr')" >> $INSTALL_DIR/runme.R </action> + <action type="shell_command">echo "install.packages('markdown')" >> $INSTALL_DIR/runme.R </action> + <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DEXSeq','ggplot2','gplots')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && + R CMD BATCH $INSTALL_DIR/runme.R > $INSTALL_DIR/install.log </action> + <action type="shell_command">cat $INSTALL_DIR/install.log</action> + </actions> + </install> + <readme>Installs some basic bioc packages for the edgeR wrapper + It's clunky but this is the only way I could get anything installed into the package_r3 R + </readme> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vst_transformation.pl Wed Jul 17 04:06:12 2013 -0400 @@ -0,0 +1,240 @@ +#!/usr/bin/perl +# vst_transformation.pl +# Joachim Jacob - joachim.jacob@vib.be - 2013 + +use strict; +use File::Basename; +use Log::Log4perl qw(:easy); + +# ---------------------- Prepping Logging -----------------------------# +######################################################################## +# Log levels: $DEBUG $INFO $WARN $ERROR $FATAL +# ConversionPattern: %d %-5p %F{1} [%M] (line %L): %m%n%n +my $log_conf = q/ + log4perl.category = ERROR, Screen + log4perl.appender.Screen.stderr=1 + log4perl.appender.Screen.layout=Log::Log4perl::Layout::PatternLayout + log4perl.appender.Screen.layout.ConversionPattern = %d %-5p %m%n + log4perl.appender.Screen = Log::Log4perl::Appender::Screen +/; + +Log::Log4perl::init( \$log_conf ); +my $logger = get_logger(); + +# ----------------- Getting parameters file ---------------------------# +######################################################################## +my ($parameters) = @ARGV; +my (%para, @repeat_blocks); +open(PARAMETERS,"<$parameters"); +while (<PARAMETERS>) { + if (/(\S+)==(.+)$/){ + $para{$1} = $2; + } +} +close(PARAMETERS); + +=Excerpt Config parameters + counttable=$counttable + outtab==$outttab + html_file==$html_file + + ##REPEAT BLOCK + #for $i, $s in enumerate( $replicates ) + replicates_$i==$s.repl_group_name + replicates_$i==$s.rep_columns + #end for + + replicates_$s.repl_group_name==$s.rep_columns + +=cut + +for my $para (keys %para){ + INFO "$para==$para{$para}"; +} + +# --------------------- KNITR SCRIPT ----------------------------------# +######################################################################## +# This script compile the HTML output from the R Markdown script below. +my $htmloutput=$para{'html_file'}; +open(KNITRSCRIPT , ">" , "knitrscript.r"); +print KNITRSCRIPT <<EOF; +require(knitr) +require(markdown) +knit("rmarkdownscript.rmd", "temp.md") +markdownToHTML("temp.md", "$htmloutput") +EOF + +# -------------------- R MARKDOWN SCRIPT ------------------------------# +######################################################################## +open(RMARKDOWN , ">>" , "rmarkdownscript.rmd"); + +## Initiating R environment +## --------------------------------------------------------------------- +print RMARKDOWN <<EOF; +VST transformation +================================ + +Loading the R environment +------------------------- + +```{r initiating environment, message=FALSE, highlight=TRUE, results="hide"} +library('DESeq') +library(reshape) +library(ggplot2) +``` +---- +EOF + +## Reading input +## Reshaping parameters +## --------------------------------------------------------------------- +my ($col_names,$row_names, $columns, $repnames, $user_col_names)=("","","","",""); + +# Getting the column numbers and replicate names +for my $parameter (keys %para){ + if ($parameter =~ /^replicates_(\S+)$/ ) { + my $rep_name=$1; + my @cols = split(",",$para{$parameter}); + # we need to subtract one from the column number if + # an column with identifiers is present. + # This column will be removed from the data when reading in. + if ( $para{'header_columns'} eq 'TRUE' ){ + foreach (@cols){ + my $colnum = $_-1; + $columns.= $colnum.","; + } + } else { + $columns.=$para{$parameter}.","; + } + # We fill a vector of replicate names as many as there are columns + $repnames.= "\"$rep_name\"," x @cols; + } +} +chop $columns; +chop $repnames; + +# If header column is present, this column contains the names of the rows. +if ( $para{'header_columns'} eq 'TRUE' ) { + $row_names = ' row.names = 1, ' +} + +# If the first row contains the column names? +if ( $para{'header_row'} eq 'TRUE' ) { + $col_names = ' header=T, '; +} else { + $user_col_names = " col.names=c("; + if ( $para{'header_columns'} eq 'TRUE' ) { $user_col_names .= '"ID",'; } + $user_col_names .= " $repnames), "; +} + +print RMARKDOWN <<EOF; +Reading input +------------- +```{r reading input, message=FALSE, highlight=TRUE} +filename="$para{'counttable'}" +raw_counts = read.csv(filename, sep="\t", $col_names $row_names stringsAsFactors=F) +raw_counts_deseqct = newCountDataSet(raw_counts[,c($columns)], factor(c($repnames))) +``` +---- +EOF + +## Applying variance stabilizing transformation +## --------------------------------------------------------------------- +print RMARKDOWN <<EOF; +Performing VST transformation +----------------------------- +```{r vst on raw counts, message=FALSE, highlight=TRUE} +raw_counts_deseqct = newCountDataSet(raw_counts[,c($columns)], factor(c($repnames))) +raw_counts_deseqct = estimateSizeFactors(raw_counts_deseqct) +raw_counts_deseqctBlind = estimateDispersions(raw_counts_deseqct,method="blind") +vsd = varianceStabilizingTransformation(raw_counts_deseqctBlind) +vst_raw_counts = exprs(vsd) +``` +---- +EOF + +## Plotting and writing results +## --------------------------------------------------------------------- +my ($colnames_out, $gg_legend, $hist_title)=("","",""); +if($para{'header_row'} eq 'TRUE' ) { + $colnames_out="col.names=NA , "; + $hist_title='main=paste("Sample",sample),'; +} else { + $colnames_out="col.names=FALSE , "; + $gg_legend= '+ theme(legend.position="none") '; + $hist_title='main="Histogram VST counts", '; +} + +print RMARKDOWN <<EOF; +Histograms +---------- +```{r plotting and writing, message=FALSE, echo=FALSE} +write.table( vst_raw_counts, file = "$para{'outtab'}", + sep = "\\t", quote = F, $colnames_out row.names=$para{'header_columns'} +) +vst_raw_counts_melted = melt(vst_raw_counts) +colnames(vst_raw_counts_melted)=c("ID","samples","value") +ggplot( data=vst_raw_counts_melted, aes(value,colour=samples)) + geom_density(alpha=0.2) + labs(x="VST of counts") $gg_legend +for(sample in colnames(vst_raw_counts)){ + hist(vst_raw_counts[,colnames(vst_raw_counts)==sample], + $hist_title breaks=80, xlab="VST counts" ) +} +``` +---- + +EOF + +## Plotting and writing results out +## --------------------------------------------------------------------- +print RMARKDOWN <<EOF; +Logging R environment +--------------------- +```{r for the log, highlight=FALSE} +sessionInfo() +``` +---- +EOF + +# -------------------- Logging scripts --------------------------------# +######################################################################## +open(my $knitrscript,"<","knitrscript.r"); +open(my $rmarkdownscript,"<","rmarkdownscript.rmd"); +while(<$knitrscript>){ + INFO $_; +} +close($knitrscript); +close($rmarkdownscript); + + +# -------------------- Assembling command ----------------------------# +######################################################################## +my $command = "R CMD BATCH knitrscript.r"; # to execute + +# --------------------- Executing command ----------------------------# +######################################################################## +run_process($command, "Knitting RMarkdown script"); + +# ------------------- Cleaning up and exiting ------------------------# +######################################################################## +$command = "rm -rf temp.md knitrscript.r knitrscript.r.Rout rmarkdownscript.rmd"; +run_process($command, "Cleaning up"); +exit 0; + +### Subroutines ### +######################################################################## +sub run_process { + my ($command, $name)= @_; + my $logger = get_logger(); + INFO "Launching process\n $command\n"; + system("$command 2>/dev/null") == 0 or die "$name failed\nExit status $?\nCommand: $command"; + if ($? == -1) { + print "failed to execute: $!\n"; + } elsif ($? & 127) { + printf "child died with signal %d, %s coredump\n", ($? & 127), ($? & 128) ? 'with' : 'without'; + } else { + printf "$name executed successfully\n", $? >> 8; + } +} + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vst_transformation.xml Wed Jul 17 04:06:12 2013 -0400 @@ -0,0 +1,73 @@ +<tool id="vsttransform" name="Variance stabilizing transformation" version="1.0.0"> + <description> + using DESeq + </description> + + <requirements> + <requirement type="package" version="3.0.1">package_r3</requirement> + <requirement type="package" version="1.0.0">r_additions</requirement> + <requirement type="package" version="2.12">biocbasics</requirement> + </requirements> + + <command interpreter="perl"> + vst_transformation.pl ${parameters} + </command> + + <inputs> + <param format="tabular" name="counttable" type="data" label="Count table" help="Count table generated by HTSeq-count on mapped RNA-seq data" /> + <param name="header_row" type="boolean" checked="TRUE" truevalue="TRUE" falsevalue="FALSE" label="Does the table has a header row" /> + <param name="header_columns" type="boolean" checked="TRUE" truevalue="TRUE" falsevalue="FALSE" label="Does the first column contains identifiers" /> + + <repeat name="replicates" title="Replicate group"> + <param name="repl_group_name" type="text" value="" size="50" label="Replicate group name"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value="_" /> </valid> + </sanitizer> + </param> + <param name="rep_columns" label="Select replicates" type="data_column" data_ref="counttable" numerical="True" + multiple="true" use_header_names="true" size="120" display="checkboxes"> + <validator type="no_options" message="Please select at least one column."/> + </param> <!-- $replicates contains a comma-separated list of number --> + </repeat> + </inputs> + + <outputs> + <data format="tabular" name="outtab" label="${tool.name} of ${on_string}"/> + <data format="html" name="html_file" label="Histogram of ${tool.name} of ${on_string}"/> + </outputs> + + <configfiles> + <configfile name="parameters"> + ## first we pass some galaxy environment variables + counttable==$counttable + header_row==$header_row + header_columns==$header_columns + outtab==$outtab + html_file==$html_file + + ##REPEAT BLOCK + #for $i, $s in enumerate( $replicates ) + replicates_$s.repl_group_name==$s.rep_columns + #end for + </configfile> + + </configfiles> + + <tests> + <test> + <param name="counttable" value="counttable1.tsv" ftype="tabular" /> + <param name="header_row" value="TRUE" /> + <param name="header_columns" value="TRUE" /> + <param name="repl_group_name" value="can" /> + <param name="rep_columns" value="2,3" /> + <output name="outtab" file="vst_transf_tabout.txt" ftype="tabular" /> + <output name="html_file" file="vst_transf_htmlout.html" ftype="html" lines_diff="6"/> + </test> + </tests> + + <help> +**Variance stabilizing transformation** + +This tool takes in raw count data per feature and applies a variance stabilizing transformation using DESeq. + </help> +</tool>