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author | bgruening |
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date | Mon, 28 Oct 2024 17:48:44 +0000 (6 weeks ago) |
parents | 282819d09a4f |
children | 48f0fb3061b1 |
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<tool id="music_construct_eset" name="Construct Expression Set Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="GPL-3.0-or-later" > <description>Create an ExpressionSet object from tabular and textual data</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ cat '$conf' >> /dev/stderr && Rscript --vanilla '$conf' ]]></command> <configfiles> <configfile name="conf" > suppressWarnings(suppressPackageStartupMessages(library(xbioc))) suppressWarnings(suppressPackageStartupMessages(library(MuSiC))) null_str_vec = function(gstr, is.str=FALSE){ tokens = unlist(as.vector(strsplit(gstr, split=","))) if (length(tokens) == 0){ if (is.str){ return(character(0)) } return(NULL) } if (length(tokens) == 1){ return(tokens[[1]]) } return(tokens) } ## Assay Data ## F rows of features and S columns of samples ## - This file is the only non-optional parameter exprs_file = '$exprs_file' exprs = as.matrix(read.table(exprs_file, header = T, sep = "\t", row.names = 1, as.is = T, check.names=FALSE)) ## Phenotype Data ## S rows of samples, and V columns of covariates (e.g. sex, age, etc.) pdata = NULL #if '$pdata_file': pdata_file = '$pdata_file' pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T, check.names=FALSE) #end if ## Annotation and Feature Data, or just a string for type of chip used annotation = null_str_vec('$annotation') if (is.null(annotation)){ annotation = character(0) } if (all(rownames(pdata) != colnames(exprs))) { stop("Number of Samples between phenotypes and assays are not the same") } ##metadata = data.frame( ## labelDescription = c( ## "Patient gender", ## "Case/Control", ## "Tumor progress"), ## row.names = c("gender", "type", "score")) metadata = as.data.frame(do.call(rbind, list( #for i, row in enumerate($metadata): #if i==0 list(ldesc='$row.label_desc', lname='$row.row_names') #else ,list(ldesc='$row.label_desc', lname='$row.row_names') #end if #end for ))) metadata\$labelDescription = unlist(metadata\$ldesc) rownames(metadata) = unlist(metadata\$lname) metadata\$ldesc = NULL metadata\$lname = NULL if (nrow(metadata)==0) { pheno_data = new("AnnotatedDataFrame", data = pdata) } else { pheno_data = new("AnnotatedDataFrame", data = pdata, varMetadata = metadata) } ## Experiment Description -- using the MIAME object experiment_data = new( "MIAME", name = null_str_vec('$expdata.name', is.str=T), lab = null_str_vec('$expdata.lab', is.str=T), contact = null_str_vec('$expdata.contact', is.str=T), title = null_str_vec('$expdata.title', is.str=T), abstract = null_str_vec('$expdata.abstract', is.str=T), url = null_str_vec('$expdata.url', is.str=T), other = list( #for i, row in enumerate($expdata.other): #if i==0 '$row.field' = null_str_vec('$row.comment', is.str=T) #else ,'$row.field' = null_str_vec('$row.comment', is.str=T) #end if #end for )) e_set = ExpressionSet(assayData = exprs, phenoData = pheno_data, experimentData = experiment_data, annotation = annotation) capture.output(print(e_set), file = '$out_txt') print(e_set) saveRDS(e_set, file= '$out_rds') </configfile> </configfiles> <inputs> <param name="exprs_file" label="Assay Data" type="data" format="tabular,tsv" help="F rows of features and S columns of samples. A Tab delimited file, with a header line and the first column has row names." /> <param name="pdata_file" label="Phenotype Data" type="data" format="tabular,tsv" optional="true" help="S rows of samples, and V columns of covariates (e.g. sex, age)" /> <param name="annotation" label="Annotation" type="text" optional="true" help="A string detailing which chip was used" > <expand macro="validator_text_and_urls" /> </param> <repeat name="metadata" title="Meta Data" min="0" max="15" > <!-- optional, so min=0 --> <param name="row_names" label="Label" type="text" help="Metadata should correspond directly to the columns of the Phenotype Data" > <expand macro="validator_text_and_urls" /> </param> <param name="label_desc" label="Label Description" type="text" > <expand macro="validator_text_and_urls" /> </param> </repeat> <section name="expdata" title="Experiment Data" > <param name="name" label="Experimenter Name" type="text" value="" optional="true" > <expand macro="validator_text_and_urls" /> </param> <param name="lab" label="Lab" type="text" value="" optional="true" > <expand macro="validator_text_and_urls" /> </param> <param name="contact" label="Contact" type="text" value="" optional="true" > <expand macro="validator_text_and_urls" /> </param> <param name="title" label="Title" type="text" value="" optional="true" > <expand macro="validator_text_and_urls" /> </param> <param name="abstract" label="Abstract" type="text" value="" optional="true" > <expand macro="validator_text_and_urls" /> </param> <param name="url" label="URL" type="text" value="" optional="true" > <expand macro="validator_text_and_urls" /> </param> <repeat name="other" title="Other Fields" min="1"> <param name="field" label="FieldName" type="text" value="notes" > <expand macro="validator_text_and_urls" /> </param> <param name="comment" label="Comment" type="text" value="Created in Galaxy" > <expand macro="validator_text_and_urls" /> </param> </repeat> </section> </inputs> <outputs> <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: General Info" /> <data name="out_rds" format="@RDATATYPE@" label="${tool.name} on ${on_string}: RData ESet Object" /> </outputs> <tests> <test expect_num_outputs="2" > <!-- Simple object --> <param name="exprs_file" value="mouse_scrna_exprs.tabular" /> <param name="pdata_file" value="mouse_scrna_pheno.tabular" /> <output name="out_txt"> <assert_contents> <has_text text="assayData: 100 features, 100 samples " /> </assert_contents> </output> </test> <test expect_num_outputs="2" > <!-- Values from the manual --> <param name="exprs_file" value="array.tsv" /> <param name="pdata_file" value="pheno.tsv" /> <param name="annotation" value="hgu95av2" /> <repeat name="metadata" > <param name="row_names" value="gender" /> <param name="label_desc" value="Patient gender" /> </repeat> <repeat name="metadata" > <param name="row_names" value="type" /> <param name="label_desc" value="Case/control status" /> </repeat> <repeat name="metadata" > <param name="row_names" value="score" /> <param name="label_desc" value="Tumor Progress on XYZ scale" /> </repeat> <section name="expdata"> <param name="name" value="Pierre Fermat" /> <param name="lab" value="Francis Galton Lab" /> <param name="contact" value="pfermat@lab.not.exist" /> <param name="title" value="Smoking-Cancer Experiment" /> <param name="abstract" value="An example ExpressionSet" /> <param name="url" value="www.lab.not.exist" /> <repeat name="other" > <param name="field" value="notes" /> <param name="comment" value="Created in Galaxy" /> </repeat> <repeat name="other" > <param name="field" value="general" /> <param name="comment" value="Some other comment" /> </repeat> </section> <output name="out_txt"> <assert_contents> <has_text text="assayData: 3 features, 2 samples " /> </assert_contents> </output> </test> </tests> <help><![CDATA[ Construct an ExpressionSet object from a variety of input attributes, such as experimentData, phenotype data, and annotations. For more options and information, consult `the manual <http://www.bioconductor.org/packages/release/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf>`_ and the `rdocumentation <https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/ExpressionSet>`_ . ]]></help> <citations> <citation type="bibtex"> @misc{falcon2007introduction, title={An introduction to bioconductor’s expressionset class}, author={Falcon, Seth and Morgan, Martin and Gentleman, Robert}, year={2007} } </citation> </citations> </tool>