# HG changeset patch
# User sigven
# Date 1671664947 0
# Node ID f6e6b6914b48403650e590da50b56c93dce490f7
# Parent  e9fcb14b0065c2c98a4ab8fb9dd8ca21d2f93bef
Uploaded

diff -r e9fcb14b0065 -r f6e6b6914b48 metascreenPre.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metascreenPre.xml	Wed Dec 21 23:22:27 2022 +0000
@@ -0,0 +1,303 @@
+<tool id="metascreenPre" name="metascreen: pre-experimental" version="0.2.6">
+  <description>Setup of drug combination screens</description>
+  <requirements>
+	   <container type="docker">sigven/metascreen:0.2.1</container>
+  </requirements>
+  <command detect_errors="aggressive"><![CDATA[
+      ln -f -s $input_data.list_of_drugs "$input_data.list_of_drugs.element_identifier" &&
+      #set drugs_csv = './' + str($input_data.list_of_drugs.element_identifier)
+
+	 ln -f -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 -f -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 -f -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 -f -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 $input_data.platemaps
+	 	ln -f -s '$pmap' '$pmap.element_identifier';
+	 #end for
+
+
+	 #set excluded_well_ids_file = ''
+      #if $dispensing_options.well_exclusion.exclude_wells
+        echo 'DUMMY_WELL' > excl_well_ids.csv &&
+	      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 $excluded_well_ids_file
+        custom_excluded_wells = readr::read_csv(
+		   	   "$excluded_well_ids_file", show_col_types = 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">
+		 <!--param name="out_dir" type="text" size="25" label="Dispensing files" value="dispFiles" /-->
+		 <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="3" min="1" max="10"/>
+		<param name="well_volume" type="integer" label="Final well volume" value="5" 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"/>
+	   	<!--data format="rdata" name="dispensingRDA" label="dispensingData - rda"/-->
+
+    <!--collection type="list" name="dispensingFiles" label="dispensingFiles">
+        <discover_datasets pattern=".csv" format="txt" directory="dispFiles" />
+    </collection-->
+    </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:
+
+set up 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>