Mercurial > repos > sigven > metascreen_post_experimental
changeset 0:c8089729e678 draft default tip
Uploaded
author | sigven |
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date | Wed, 21 Dec 2022 23:24:32 +0000 |
parents | |
children | |
files | metascreenPost.xml |
diffstat | 1 files changed, 125 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metascreenPost.xml Wed Dec 21 23:24:32 2022 +0000 @@ -0,0 +1,125 @@ +<tool id="metascreenPost" name="metascreen: post-experimental" version="0.2.6"> + <description>Consolidation of drug combination screens</description> + <requirements> + <container type="docker">sigven/metascreen:0.2.1</container> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + + ln -f -s $input_data.barcode_reference "$input_data.barcode_reference.element_identifier" && + #set barcode_reference_csv = './' + str($input_data.barcode_reference.element_identifier) + + ln -f -s $input_data.dispensing_data "$input_data.dispensing_data.element_identifier" && + #set dispensing_data_tsv = './' + str($input_data.dispensing_data.element_identifier) + + #for $raw_assay_file in $input_data.assay_raw + ln -f -s '$raw_assay_file' '$raw_assay_file.element_identifier'; + #end for + + R -e 'suppressPackageStartupMessages(library(metascreen)); + + barcode_reference <- read.csv( + file = "$barcode_reference_csv", + check.names = FALSE, + colClasses = c("PlateID"="character"), + na.strings = "", + encoding = "UTF-8"); + + dispData <- as.data.frame( + readr::read_tsv( + file = "$dispensing_data_tsv", + col_names = TRUE, show_col_types = FALSE + ) + ); + + dispData[,"Plate.Number"] <- + as.factor(dispData[,"Plate.Number"]); + dispData[,"Combination.ID"] <- + as.integer(dispData[,"Combination.ID"]); + + rfs = list(); + #for $raw_assay_file in $input_data.assay_raw + + rfs = append( + rfs, + metascreen::readRAWData( + .readfrom = "$raw_assay_file.element_identifier", + .format = "$input_data.assay_format" + ) + ); + #end for + + names(rfs) <- stringr::str_replace(names(rfs),".csv",""); + + clData <- metascreen::consolidateData( + dispensingData = dispData, + rawMeasurements = rfs, + .barcodeReference = barcode_reference); + + + df = as.data.frame(clData[["consolidated"]]); + readr::write_tsv( + df, file="$consolidatedData", col_names=T, quote="none");' 2>&1 + + ]]></command> + <inputs> + + <section name="input_data" title="User-defined input files - see below for formatting requirements" expanded="true"> + <param name="barcode_reference" type="data" format="txt" label="Barcode reference (CSV)" multiple="false"/> + <param name="dispensing_data" type="data" format="txt" label="Dispensing data (TSV)" multiple="false"/> + <param name="assay_raw" type="data" format="txt" label="Raw assay measurement data (CSV)" multiple="true"/> + <!--param name="convert_platemap_format" type="boolean" label="Convert platemap to a source plate format" truevalue="T" falsevalue="F" checked="false"/--> + <param name="assay_format" type="select" label="Assay measurement format" display="radio" multiple="false"> + <option value="EnVision">EnVision</option> + <option value="raw">raw</option> + <option value="VICTOR">VICTOR</option> + </param> + </section> + + </inputs> + <outputs> + <data format="txt" name="consolidatedData" label="consolidatedData - tsv"/> + </outputs> + + + <help><![CDATA[ +.. class:: infomark + +Limitations etc: + +----- + +**Dataset formats** + +The input datasets are in text_ (CSV/TSV) format format. The output dataset is also in text_ (TSV) formats. + +.. _text: ${static_path}/formatHelp.html#text + +Specific input file requirements: + +- **List of raw assay measurements** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file + + TODO: Briefly describe requirements for *raw* and other available formats for raw assay measurements (EnVision, VICTOR) + +- **Plate barcode reference.** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file + + Provides the sample names used in the drug screen and the corresponding plate id and set + Format: ['PlateID', 'Set', 'Number','Sample]. + An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/platebarcode.csv + +- **Dispensing data** - TSV (output from *metascreen: pre-experimental* module) + +----- + +**What it does** + +The intention of the *post-experimental* module of metascreen is to consolidate the raw assay +measurements and the dispensing data (the latter produced as output by the *pre-experimental* module +of metascreen). The module will build a final reference data set, to be used for +any downstream analysis of the drug sensitivity screen. A barcode reference list with the names of +the samples used in the drug screen is necessary so that these can be associated to the +corresponding plate id and set. + +]]> + </help> + +</tool>