Mercurial > repos > sigven > metascreen_pre_experimental

changeset 7:3a345b6f5d3d draft default tip

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Deleted selected files
author sigven
date Wed, 21 Dec 2022 23:22:36 +0000
parents f6e6b6914b48
children
files metascreen.xml
diffstat 1 files changed, 0 insertions(+), 294 deletions(-) [+]
line wrap: on
line diff
--- 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>