# HG changeset patch # User sigven # Date 1668113390 0 # Node ID c5deb8fae68673ff54bb521f131d7d870b88b8b3 # Parent 600a6823fcd4d5cad81ace7d04b8f175f092836b Deleted selected files diff -r 600a6823fcd4 -r c5deb8fae686 metascreen.xml --- a/metascreen.xml Thu Nov 10 20:47:57 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,292 +0,0 @@ - - Pre-experimental setup of drug combination screens - excl_well_ids.csv && - #set excluded_well_ids_file = './excl_well_ids.csv' - #end if - - R -e 'suppressPackageStartupMessages(library(metascreen)); - - custom_excluded_wells = NULL; - #if $excluded_well_ids_file - custom_excluded_wells = read.csv( - "$excluded_well_ids_file", stringsAsFactors = F, header = F); - custom_excluded_wells = custom_excluded_wells[[1]]; - #end if - - list_of_drugs_raw <- read.csv( - file = "$drugs_csv", - check.names = FALSE, - na.strings = "", - dec = ".", encoding = "UTF-8"); - list_of_volumes_raw <- read.csv( - file = "$volumes_csv", - check.names = FALSE, - na.strings = "", - dec = ".", encoding = "UTF-8"); - list_of_doses_raw <- read.csv( - file = "$doses_csv", - check.names = FALSE, - na.strings = "", - dec = ".", encoding = "UTF-8"); - list_of_controls_raw <- read.csv( - file = "$ctrls_csv", - check.names = FALSE, - na.strings = "", - dec = ".", encoding = "UTF-8"); - list_of_stock_cons_raw <- read.csv( - file = "$stock_cons_csv", - check.names = FALSE, - na.strings = "", - dec = ".", encoding = "UTF-8"); - - listofDoses <- - metascreen::generateListofDoses( - list_of_doses_raw, - .dropCol = TRUE); - - - sourcePlate = data.frame(); - #for $pmap in $input_data.platemaps - - sourcePlate = dplyr::bind_rows( - sourcePlate, - metascreen::importPlateMap( - "$pmap.element_identifier", - .fileFormat = "PlateMap", - galaxy = TRUE, - .sourcePlateConv = $input_data.convert_platemap_format - ) - ); - #end for - - combine_doses = c(1:min(unique(table(listofDoses[,"Drug"])))); - exclude_outer_wells = FALSE; - - #if $dispensing_options.well_exclusion.exclude_wells - exclude_outer_wells = $dispensing_options.well_exclusion.outer_wells; - #end if - - #if $combination_options.combo_design.type_combination == "all" - #if $combination_options.combo_design.inner_dosing - combine_doses = c(2:(min(unique(table(listofDoses[,"Drug"])))-1)); - #end if - #end if - - add_untreated = NULL; - #if $dispensing_options.add_untreated.untreated - add_untreated = list( - name = "$dispensing_options.add_untreated.untreated_name", - replicates = $dispensing_options.add_untreated.untreated_replicates); - #end if - - - listofExWells <- - metascreen::excludeWells( - plateType = $input_data.plateformat, - wells = custom_excluded_wells, - outer.wells = exclude_outer_wells); - - - listofCombinations <- - metascreen::combineDrugs( - listofDoses, - .combineDoses = combine_doses, - .noReplicates = $combination_options.num_replicates, - .drugRepAttrib = "$combination_options.combo_design.type_combination"); - - - dispensingData <- - metascreen::generateDispensingData( - listofCombinations, - list_of_drugs_raw, - listofDoses, - list_of_volumes_raw, - list_of_controls_raw, - list_of_stock_cons_raw, - sourcePlate, - listofExWells, - .ctrlReplicates = $dispensing_options.num_control_replicates, - .addUntreated = add_untreated, - .finalWellVolume = $dispensing_options.well_volume, - .plateFormat = $input_data.plateformat, - .destinationPlateID = "$dispensing_options.dest_plate_ID", - .randomizeDispensing = $dispensing_options.randomise_dispensing, - .probeDispensing = $dispensing_options.probe_dispensing); - - df = as.data.frame(dispensingData[["output"]]); - readr::write_tsv(listofCombinations,file="$doseComb",col_names=T, quote="none"); - readr::write_tsv(df,file="$dispensingDF", col_names = T, quote = "none");' 2>&1 - - ]]> - - -
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- - - - - - - - `_ file - - Provides a list of all the doses for each drug used in - a drug sensitivity screen. The list needs to include a column with the drug number, - drug name, one or multiple columns for the doses, and a column with the unit. - ['Number', 'Drug', '6th Dose', ..., '1st Dose', 'Unit']. - An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofdoses.csv - -- **List of drugs.** - `CSV `_ file - - Provides a list of drugs used in the drug screen. The list - needs to include a column with a unique drug number / id for each drug, the - drug name and the CAS number. ['ID', 'NAME', 'CAS_NUMBER']. For custom - compunds without CAS number, include column, but leave field empty. - An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofdrugs.csv - -- **List of stock concentrations.** - A `CSV `_ file - - Provides a list of the stock concentrations - for each drug used in the drug screen. If the stock concentrations are not - known, use the highest dose. The list needs to include column with the unique - drug number / id, the drug name, the stock concentration and the concentration unit. - ['NUMBER', 'NAME', 'CONCENTRATION', 'UNIT']. - An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofstockconcentrations.csv - - - **List of controls.** - A `CSV `_ file - - Provides the controls to be used in a drug - screen. The list needs to include a column with the name, CAS number, - dose, unit, the source plate from which the control is dispensed from and the - volume. ['NAME', 'CAS_NUMBER', 'DOSE', 'UNIT', 'SOURCE_PLATE', 'VOLUME']. - An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofctrls.csv - - - **List of drug volumes.** - A `CSV `_ file - - Provides the volumes for each drug that - have been or will be dispensed. The list follows the same format as the - list of drug doses. The list needs to include a column with the drug number, - drug name, one or multiple columns with doses, and a column with the unit. - ['Number', 'Drug', 'Vol 6th Dose', ..., 'Vol 1st Dose', 'Unit']. - An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofvolumes.csv - - - - **plateMap** - XML file (s) - - One or more plate map files with the contents (usually compounds/drugs) of the - source plate from which drugs are dispensed from. Plate maps can currently be imported - using .PlateMap (XML files) provided by the IncuCyte® Plate Map Editor. **IMPORTANT: when uploading - PlateMap files to Galaxy, please make sure you denote file 'Type' as XML.** - - An example is shown with https://github.com/Enserink-lab/metascreen/blob/main/inst/extdata/library/C008.PlateMap - ------ - -**What it does** - -The *pre-experimental* modules of metascreen is intended to serve the following purposes: - -allowing to set-up a drug combination screens by (a) generating drug combinations from a list of drugs and -(b) distributing those drug combinations across a number of experimental plates. (c) generating instructions -for dispensing robots for the creation of those experimental plates. - - - - - - -]]> - - -