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1 <tool id="screenwerkPost" name="screenwerk: post-experimental" version="0.2.6">
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2 <description>Consolidation of drug combination screens</description>
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3 <requirements>
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4 <container type="docker">sigven/metascreen:0.2.1</container>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7
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8 ln -f -s $input_data.barcode_reference "$input_data.barcode_reference.element_identifier" &&
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9 #set barcode_reference_csv = './' + str($input_data.barcode_reference.element_identifier)
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10
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11 ln -f -s $input_data.dispensing_data "$input_data.dispensing_data.element_identifier" &&
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12 #set dispensing_data_tsv = './' + str($input_data.dispensing_data.element_identifier)
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13
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14 #for $raw_assay_file in $input_data.assay_raw
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15 ln -f -s '$raw_assay_file' '$raw_assay_file.element_identifier';
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16 #end for
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17
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18 R -e 'suppressPackageStartupMessages(library(metascreen));
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19
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20 barcode_reference <- read.csv(
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21 file = "$barcode_reference_csv",
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22 check.names = FALSE,
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23 colClasses = c("PlateID"="character"),
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24 na.strings = "",
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25 encoding = "UTF-8");
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26
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27 dispData <- as.data.frame(
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28 readr::read_tsv(
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29 file = "$dispensing_data_tsv",
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30 col_names = TRUE, show_col_types = FALSE
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31 )
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32 );
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33
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34 dispData[,"Plate.Number"] <-
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35 as.factor(dispData[,"Plate.Number"]);
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36 dispData[,"Combination.ID"] <-
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37 as.integer(dispData[,"Combination.ID"]);
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38
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39 rfs = list();
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40 #for $raw_assay_file in $input_data.assay_raw
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41
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42 rfs = append(
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43 rfs,
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44 metascreen::readRAWData(
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45 .readfrom = "$raw_assay_file.element_identifier",
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46 .format = "$input_data.assay_format"
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47 )
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48 );
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49 #end for
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50
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51 names(rfs) <- stringr::str_replace(names(rfs),".csv","");
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52
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53 clData <- metascreen::consolidateData(
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54 dispensingData = dispData,
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55 rawMeasurements = rfs,
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56 .barcodeReference = barcode_reference);
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57
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58
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59 df = as.data.frame(clData[["consolidated"]]);
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60 readr::write_tsv(
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61 df, file="$consolidatedData", col_names=T, quote="none");' 2>&1
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62
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63 ]]></command>
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64 <inputs>
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65
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66 <section name="input_data" title="User-defined input files - see below for formatting requirements" expanded="true">
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67 <param name="barcode_reference" type="data" format="txt" label="Barcode reference (CSV)" multiple="false"/>
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68 <param name="dispensing_data" type="data" format="txt" label="Dispensing data (TSV)" multiple="false"/>
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69 <param name="assay_raw" type="data" format="txt" label="Raw assay measurement data (CSV)" multiple="true"/>
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70 <!--param name="convert_platemap_format" type="boolean" label="Convert platemap to a source plate format" truevalue="T" falsevalue="F" checked="false"/-->
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71 <param name="assay_format" type="select" label="Assay measurement format" display="radio" multiple="false">
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72 <option value="EnVision">EnVision</option>
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73 <option value="raw">raw</option>
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74 <option value="VICTOR">VICTOR</option>
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75 </param>
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76 </section>
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77
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78 </inputs>
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79 <outputs>
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80 <data format="txt" name="consolidatedData" label="consolidatedData - tsv"/>
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81 </outputs>
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82
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83
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84 <help><![CDATA[
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85 .. class:: infomark
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86
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87 Limitations etc:
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88
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89 -----
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90
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91 **Dataset formats**
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92
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93 The input datasets are in text_ (CSV/TSV) format format. The output dataset is also in text_ (TSV) formats.
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94
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95 .. _text: ${static_path}/formatHelp.html#text
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96
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97 Specific input file requirements:
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98
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99 - **List of raw assay measurements** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
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100
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101 TODO: Briefly describe requirements for *raw* and other available formats for raw assay measurements (EnVision, VICTOR)
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102
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103 - **Plate barcode reference.** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
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104
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105 Provides the sample names used in the drug screen and the corresponding plate id and set
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106 Format: ['PlateID', 'Set', 'Number','Sample].
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107 An example is shown with https://raw.githubusercontent.com/Enserink-lab/screenwerk/main/inst/extdata/library/platebarcode.csv
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108
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109 - **Dispensing data** - TSV (output from *metascreen: pre-experimental* module)
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110
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111 -----
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112
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113 **What it does**
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114
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115 The intention of the *post-experimental* module of metascreen is to consolidate the raw assay
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116 measurements and the dispensing data (the latter produced as output by the *pre-experimental* module
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117 of metascreen). The module will build a final reference data set, to be used for
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118 any downstream analysis of the drug sensitivity screen. A barcode reference list with the names of
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119 the samples used in the drug screen is necessary so that these can be associated to the
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120 corresponding plate id and set.
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121
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122 ]]>
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123 </help>
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124 <citations>
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125 <!-- Example of annotating a citation using a DOI. -->
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126 <citation type="doi">10.1093/bioinformatics/btac840</citation>
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127 <!-- Example of annotating a citation using a BibTex entry. -->
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128 </citations>
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129 </tool>
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