Mercurial > repos > sigven > metascreen_pre_experimental
diff metascreen.xml @ 7:3a345b6f5d3d draft default tip
Deleted selected files
| author | sigven |
|---|---|
| date | Wed, 21 Dec 2022 23:22:36 +0000 |
| parents | f6e6b6914b48 |
| children |
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--- a/metascreen.xml Wed Dec 21 23:22:27 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,294 +0,0 @@ -<tool id="metascreenPre" name="metascreen: pre-experimental" version="0.2.4"> - <description>Pre-experimental setup of drug combination screens</description> - <requirements> - <container type="docker">sigven/metascreen:0.2.0</container> -</requirements> - <command detect_errors="aggressive"><![CDATA[ - ln -s $input_data.list_of_drugs "$input_data.list_of_drugs.element_identifier" && - #set drugs_csv = './' + str($input_data.list_of_drugs.element_identifier) - - ln -s $input_data.list_of_volumes "$input_data.list_of_volumes.element_identifier" && - #set volumes_csv = './' + str($input_data.list_of_volumes.element_identifier) - - ln -s $input_data.list_of_doses "$input_data.list_of_doses.element_identifier" && - #set doses_csv = './' + str($input_data.list_of_doses.element_identifier) - - ln -s $input_data.list_of_ctrls "$input_data.list_of_ctrls.element_identifier" && - #set ctrls_csv = './' + str($input_data.list_of_ctrls.element_identifier) - - ln -s $input_data.list_of_stock_cons "$input_data.list_of_stock_cons.element_identifier" && - #set stock_cons_csv = './' + str($input_data.list_of_stock_cons.element_identifier) - - #for $pmap in $input_data.platemaps - ln -s '$pmap' '$pmap.element_identifier'; - #end for - - - #set excluded_well_ids_file = '' - #if $dispensing_options.well_exclusion.exclude_wells - echo $dispensing_options.well_exclusion.well_ids | sed 's/__cn__/\n/g' > 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", - .sourcePlateConv = TRUE - ) - ); - #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 - - ]]></command> - <inputs> - - <section name="input_data" title="User-defined input files - see below for strict formatting requirements" expanded="true"> - <param name="list_of_doses" type="data" format="txt" label="List of drug doses (CSV)" multiple="false"/> - <param name="list_of_drugs" type="data" format="txt" label="List of drugs (CSV)" multiple="false"/> - <param name="list_of_volumes" type="data" format="txt" label="List of volumes (CSV)" multiple="false"/> - <param name="list_of_ctrls" type="data" format="txt" label="List of controls (CSV)" multiple="false"/> - <param name="list_of_stock_cons" type="data" format="txt" label="List of stock concentrations (CSV)" multiple="false"/> - <param name="platemaps" type="data" format="xml" label="PlateMap file (XML)" 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="plateformat" type="select" label="Plate format" display="radio" multiple="false"> - <option value="6">6</option> - <option value="12">12</option> - <option value="24">24</option> - <option value="48">48</option> - <option value="96">96</option> - <option value="384">384</option> - <option value="1536">1536</option> - </param> - </section> - - <section name="combination_options" title="Options - drug combination design" expanded="true"> - <conditional name="combo_design"> - <param name="type_combination" type="select" display="radio" multiple="false" label="Type of dose combinations"> - <option value="all">All - both single treatments and combination treatments</option> - <option value="single">Single - only single treatments</option> - </param> - <when value="all"> - <param name="inner_dosing" type="boolean" label="Exclude lowest and highest dose (inner dosing only)" truevalue="T" falsevalue="F" checked="false"/> - </when> - </conditional> - <param type="integer" name="num_replicates" label="Number of replicates for each dose combination" value="3" min="1" max="20"/> - </section> - <section name="dispensing_options" title="Options - dispensing layout" expanded="true"> - <conditional name="well_exclusion"> - <param name="exclude_wells" type="boolean" label="Exclusion of wells" truevalue="T" falsevalue="F" checked="false"/> - <when value="T"> - <param name="well_ids" type="text" label="Custom set of well identifiers to exclude (one per line):" area="true"/> - <param name="outer_wells" type="boolean" label="Exclude all outer wells" truevalue="T" falsevalue="F" checked="true"/> - </when> - </conditional> - <param name="num_control_replicates" type="integer" label="Number of control replicates" value="5" min="1" max="10"/> - <param name="well_volume" type="integer" label="Final well volume" value="10" min="1" max="500"/> - <param name="randomise_dispensing" type="boolean" label="Randomise dispensing" truevalue="T" falsevalue="F" checked="true"/> - <param name="probe_dispensing" type="boolean" label="Probe dispensing" truevalue="T" falsevalue="F" checked="false"/> - <param name="dest_plate_ID" type="text" value="PLATE_012" label="A unique destination plate ID - for destination plate barcode"/> - <conditional name="add_untreated"> - <param name="untreated" type="boolean" label="Add untreated" truevalue="T" falsevalue="F" checked="true"/> - <when value="T"> - <param name="untreated_name" type="text" label="Identifier (name) for untreated" value="Untreated"/> - <param name="untreated_replicates" type="integer" label="Number of untreated replicates" value="5" min="1" max="500"/> - </when> - </conditional> - - </section> - </inputs> - <outputs> - <!--data format="xlsx" name="output_xlsx" label="crisprFPA - xlsx"/--> - <data format="txt" name="doseComb" label="doseCombinations - tsv"/> - <data format="txt" name="dispensingDF" label="dispensingData - tsv"/> - </outputs> - - - <help><![CDATA[ -.. class:: infomark - -Limitations etc: - ------ - -**Dataset formats** - -The input datasets are in text_ (CSV) format and in XML format. The output datasets are also in text_ formats. - -.. _text: ${static_path}/formatHelp.html#text - -Specific input file requirements: - -- **List of drug doses** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ 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 <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ 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 <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ 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 <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ 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 <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ 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. - - - - - - -]]> - </help> - -</tool>