Mercurial > repos > bgruening > music_construct_eset
diff construct_eset.xml @ 0:2cfd0db49bbc draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
| author | bgruening |
|---|---|
| date | Sun, 12 Sep 2021 19:49:12 +0000 |
| parents | |
| children | be91cb6f48e7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/construct_eset.xml Sun Sep 12 19:49:12 2021 +0000 @@ -0,0 +1,211 @@ +<tool id="music_construct_eset" name="Construct Expression Set Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" + profile="20.05" 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[ +Rscript --vanilla '$conf' +]]></command> + <configfiles> + <configfile name="conf" > + +suppressWarnings(suppressPackageStartupMessages(library(xbioc))) +suppressWarnings(suppressPackageStartupMessages(library(MuSiC))) + +null_str_vec = function(gstr){ + tokens = unlist(as.vector(strsplit(gstr, split=","))) + if (length(tokens) == 0){ + return(NULL) + } + if (length(tokens) == 1){ + return(tokens[[1]]) + } + return(tokens) +} + +## Assay Data +## F rows of features and S columns of samples +## - This file is the only non-optional parameter +exprs_file = '$exprs_file' +exprs = as.matrix(read.table(exprs_file, header = T, sep = "\t", + row.names = 1, as.is = T)) +## 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) +#end if +## Annotation and Feature Data, or just a string for type of chip used +annotation = null_str_vec('$annotation') + +if (all(rownames(pdata) != colnames(exprs))) { + stop("Number of Samples between phenotypes and assays are not the same") +} + +##metadata = data.frame( +## labelDescription = c( +## "Patient gender", +## "Case/Control", +## "Tumor progress"), +## row.names = c("gender", "type", "score")) +metadata = as.data.frame(do.call(rbind, list( +#for i, row in enumerate($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) { + metadata = NULL +} + +pheno_data = new("AnnotatedDataFrame", data = pdata, varMetadata = metadata) + +## Experiment Description -- using the MIAME object +experiment_data = new( + "MIAME", + name = null_str_vec('$expdata.name'), + lab = null_str_vec('$expdata.lab'), + contact = null_str_vec('$expdata.contact'), + title = null_str_vec('$expdata.title'), + abstract = null_str_vec('$expdata.abstract'), + url = null_str_vec('$expdata.url'), + other = list( +#for i, row in enumerate($expdata.other): + #if i==0 + '$row.field' = null_str_vec('$row.comment') + #else + ,'$row.field' = null_str_vec('$row.comment') + #end if +#end for +)) + +e_set = ExpressionSet(assayData = exprs, + phenoData = pheno_data, + experimentData = experiment_data, + annotation = annotation) + +capture.output(print(e_set), file = '$out_tab') +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" > + <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_tab" format="tabular" label="${tool.name} on ${on_string}: General Info" /> + <data name="out_rds" format="rdata.eset" label="${tool.name} on ${on_string}: RData ESet Object" /> + </outputs> + <tests> + <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_tab"> + <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> \ No newline at end of file