Mercurial > repos > iuc > sleuth
changeset 1:d3e447dd52c8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
| author | iuc |
|---|---|
| date | Wed, 07 Jun 2023 11:47:30 +0000 |
| parents | 5f1cb4c28d73 |
| children | d6b5fc94062c |
| files | macros.xml sleuth.R sleuth.xml test-data/design.tab test-data/test02_density.pdf test-data/test02_pca.pdf |
| diffstat | 6 files changed, 156 insertions(+), 47 deletions(-) [+] |
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--- a/macros.xml Thu Jun 01 07:56:00 2023 +0000 +++ b/macros.xml Wed Jun 07 11:47:30 2023 +0000 @@ -8,7 +8,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">0.30.1</token> - <token name="@SUFFIX_VERSION@">0</token> + <token name="@SUFFIX_VERSION@">1</token> <token name="@PROFILE@">20.01</token> <xml name="citations"> <citations>
--- a/sleuth.R Thu Jun 01 07:56:00 2023 +0000 +++ b/sleuth.R Wed Jun 07 11:47:30 2023 +0000 @@ -26,39 +26,67 @@ # Collect arguments from command line parser <- ArgumentParser(description = "Sleuth R script") -parser$add_argument("--factorLevel", action = "append", required = TRUE) +parser$add_argument("--factorLevel", action = "append", required = FALSE) parser$add_argument("--factorLevel_counts", action = "append", - required = TRUE) -parser$add_argument("--factorLevel_n", action = "append", required = TRUE) -parser$add_argument("--cores", type = "integer", required = TRUE) + required = FALSE) +parser$add_argument("--factorLevel_n", action = "append", required = FALSE) +parser$add_argument("--cores", type = "integer", required = FALSE) parser$add_argument("--normalize", action = "store_true", required = FALSE) -parser$add_argument("--nbins", type = "integer", required = TRUE) -parser$add_argument("--lwr", type = "numeric", required = TRUE) -parser$add_argument("--upr", type = "numeric", required = TRUE) +parser$add_argument("--nbins", type = "integer", required = FALSE) +parser$add_argument("--lwr", type = "numeric", required = FALSE) +parser$add_argument("--upr", type = "numeric", required = FALSE) +parser$add_argument("--metadata_file", + action = "append", + required = FALSE) +parser$add_argument("--experiment_design", required = FALSE) args <- parser$parse_args() -all_files <- args$factorLevel_counts +if (args$experiment_design == "complex") { + ## Complex experiment design + ############################ -conditions <- c() -for (x in seq_along(args$factorLevel)) { - temp <- append(conditions, rep(args$factorLevel[[x]])) - conditions <- temp -} + s2c <- + read.table(file = args$metadata_file, + header = TRUE, + sep = "\t") + paths <- c() + for (x in s2c$data_filename) { + paths <- c(paths, paste("./kallisto_outputs/", x, sep = "")) + } + for (f in paths) { + file.rename(f, gsub(".fastq.*", "", f)) + file.rename(f, paste(gsub(".fastq.*", "", f), ".h5", sep = "")) + } + s2c$path <- paste(gsub(".fastq.*", ".h5", paths), ".h5", sep = "") + + so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1) + so <- sleuth_fit(so) -sample_names <- all_files %>% - str_replace(pattern = "\\.tab", "") +} else { + ## Simple experiment design + ########################### + + conditions <- c() + for (x in seq_along(args$factorLevel)) { + temp <- append(conditions, rep(args$factorLevel[[x]])) + conditions <- temp + } -design <- - data.frame(list( - sample = sample_names, - condition = conditions, - path = all_files - )) -so <- sleuth_prep(design, - cores = args$cores, - normalize = args$normalize) + sample_names <- + gsub(".fastq.+", "", basename(args$factorLevel_counts)) + + design <- + data.frame(list( + sample = sample_names, + condition = conditions, + path = args$factorLevel_counts + )) + so <- sleuth_prep(design, + cores = args$cores, + normalize = args$normalize) +} so <- sleuth_fit( so,
--- a/sleuth.xml Thu Jun 01 07:56:00 2023 +0000 +++ b/sleuth.xml Wed Jun 07 11:47:30 2023 +0000 @@ -21,23 +21,38 @@ </stdio> <version_command><![CDATA[echo $(R --version | grep version | grep -v GNU)", sleuth version" $(R --vanilla --slave -e "library(sleuth); cat(sessionInfo()\$otherPkgs\$sleuth\$Version)" 2> /dev/null | grep -v -i "WARNING: ")]]></version_command> <command><![CDATA[ - #set $factor_levels = list() + #import os + mkdir -p './kallisto_outputs' && #set $cond_files = list() - #set $cond_n_files = list() - #for $level in $rep_factorLevel - $factor_levels.append(str($level.factorLevel)) - $cond_n_files.append(len(str($level.countsFile).split(","))) - #for $i, $count in enumerate(str($level.countsFile).split(",")) - #set $fname = str($level.factorLevel) + "_" + str($i) + '.h5' - ln -s '${count}' "${fname}" && - $cond_files.append($fname) + #if $experiment_design.selector == "single" + #set $factor_levels = list() + #set $cond_n_files = list() + #for $level in $experiment_design.rep_factorLevel + $factor_levels.append(str($level.factorLevel)) + $cond_n_files.append(len(str($level.countsFile).split(","))) + #for $i, $count in enumerate(str($level.countsFile).split(",")) + #set $fname = str($level.factorLevel) + "_" + str($i) + '.h5' + #set $output_path = "/".join(['./kallisto_outputs',$fname]) + ln -s '${count}' $output_path && + $cond_files.append($output_path) + #end for #end for - #end for + #else + #for $count in $experiment_design.countsFile + #set $output_path = "/".join(['./kallisto_outputs',$count.element_identifier]) + ln -s '${count}' $output_path && + $cond_files.append($output_path) + #end for + #end if Rscript '${__tool_directory__}/sleuth.R' - #for $i, $factor in enumerate($factor_levels) - --factorLevel $factor - --factorLevel_n $cond_n_files[$i] - #end for + #if $experiment_design.selector == "single" + #for $i, $factor in enumerate($factor_levels) + --factorLevel $factor + --factorLevel_n $cond_n_files[$i] + #end for + #else + --metadata_file $experiment_design.metadata_file + #end if #for $file in $cond_files --factorLevel_counts $file #end for @@ -46,17 +61,30 @@ --nbins $advanced_options.nbins --lwr $advanced_options.lwr --upr $advanced_options.upr + --experiment_design $experiment_design.selector ]]></command> <inputs> - <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> - <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" - help="Only letters, numbers and underscores will be retained in this field"> - <sanitizer> - <valid initial="string.letters,string.digits"><add value="_" /></valid> - </sanitizer> + <conditional name="experiment_design"> + <param name="selector" type="select" label="Experiment design" help="If you have multiple experimental conditions, you should use propably the complex design mode. In the help section you can find more information."> + <option value="single">Simple design mode (one experimental factor)</option> + <option value="complex">Complex design mode (two experimental factors)</option> </param> - <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/> - </repeat> + <when value="single"> + <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> + <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/> + </repeat> + </when> + <when value="complex"> + <param name="countsFile" type="data_collection" format="h5" multiple="true" label="Counts file(s)"/> + <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about it in the help section" /> + </when> + </conditional> <section name="advanced_options" title="Advanced options" expanded="true"> <param argument="normalization" type="boolean" truevalue="--normalize" falsevalue="" checked="true" label="Normalize data" help="If this is set to false, bootstraps will not be read and transformation of the data will not be done. This should @@ -68,6 +96,7 @@ <param argument="upr" type="float" min="0" max="1" value="0.75" label="UPR" help="The upper range of variances within each bin that should be included for the shrinkage procedure." /> </section> + </inputs> <outputs> <data name="sleuth_table" from_work_dir="sleuth_table.tab" format="tabular" label="${tool.name} on ${on_string}: DE table"> @@ -104,6 +133,35 @@ <output name="pca_plot" file="test01_pca.pdf" ftype="pdf" compare="sim_size"/> <output name="density_plot" file="test01_density.pdf" ftype="pdf" compare="sim_size"/> </test> + <test expect_num_outputs="3"> + <conditional name="experiment_design"> + <param name="selector" value="complex"/> + <param name="countsFile"> + <collection type="list"> + <element name="kallisto_output_01.h5" ftype="h5" value="kallisto_output_01.h5"/> + <element name="kallisto_output_02.h5" ftype="h5" value="kallisto_output_02.h5"/> + <element name="kallisto_output_03.h5" ftype="h5" value="kallisto_output_03.h5"/> + <element name="kallisto_output_04.h5" ftype="h5" value="kallisto_output_04.h5"/> + </collection> + </param> + <param name="metadata_file" value="design.tab"/> + </conditional> + <section name="advanced_options"> + <param name="normalization" value="true"/> + <param name="nbins" value="100"/> + <param name="lwr" value="0.25"/> + <param name="upr" value="0.75"/> + </section> + <output name="sleuth_table" ftype="tabular"> + <assert_contents> + <has_size value="756310" delta="100"/> + <has_text text="ENST00000394894.8"/> + <has_text text="ENST00000524187.1"/> + </assert_contents> + </output> + <output name="pca_plot" file="test02_pca.pdf" ftype="pdf" compare="sim_size"/> + <output name="density_plot" file="test02_density.pdf" ftype="pdf" compare="sim_size"/> + </test> </tests> <help><![CDATA[ @@ -123,6 +181,24 @@ These can serve as proxies for technical replicates, allowing for an ascertainment of the variability in estimates due to the random processes underlying RNA-Seq as well as the statistical procedure of read assignment. +.. class:: infomark + +**Experimental design tabular input for complex experimental designs** + +The experimental design input should have this format: + + :: + + data_filename condition sample + finename_01.fastq.gz condition1 replicate1 + filename_02.fastq.gz condition1 replicate2 + filename_03.fastq.gz condition2 replicate1 + filename_04.fastq.gz condition2 replicate2 + + +The tabular file **requires to have the same column names** as the example (data_file, condition, sample). The data file column correspond to original FASTQ filenames uploaded to Galaxy. +Condition includes the information about the first factor, and sample includes information about the second factor. **Only alphanumeric characters, undescores and dots are allowed**. + ]]></help> <expand macro="citations" /> </tool>