<tool id="screenwerkPost" name="screenwerk: 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/screenwerk/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>
  <citations>
     <!-- Example of annotating a citation using a DOI. -->
     <citation type="doi">10.1093/bioinformatics/btac840</citation>
     <!-- Example of annotating a citation using a BibTex entry. -->
  </citations>
</tool>