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comparison metascreenPost.xml @ 0:44fa507ac6e7 draft default tip

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author sigven
date Mon, 13 Nov 2023 13:46:18 +0000
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1 <tool id="screenwerkPost" name="screenwerk: post-experimental" version="0.2.6">
2 <description>Consolidation of drug combination screens</description>
3 <requirements>
4 <container type="docker">sigven/metascreen:0.2.1</container>
5 </requirements>
6 <command detect_errors="aggressive"><![CDATA[
7
8 ln -f -s $input_data.barcode_reference "$input_data.barcode_reference.element_identifier" &&
9 #set barcode_reference_csv = './' + str($input_data.barcode_reference.element_identifier)
10
11 ln -f -s $input_data.dispensing_data "$input_data.dispensing_data.element_identifier" &&
12 #set dispensing_data_tsv = './' + str($input_data.dispensing_data.element_identifier)
13
14 #for $raw_assay_file in $input_data.assay_raw
15 ln -f -s '$raw_assay_file' '$raw_assay_file.element_identifier';
16 #end for
17
18 R -e 'suppressPackageStartupMessages(library(metascreen));
19
20 barcode_reference <- read.csv(
21 file = "$barcode_reference_csv",
22 check.names = FALSE,
23 colClasses = c("PlateID"="character"),
24 na.strings = "",
25 encoding = "UTF-8");
26
27 dispData <- as.data.frame(
28 readr::read_tsv(
29 file = "$dispensing_data_tsv",
30 col_names = TRUE, show_col_types = FALSE
31 )
32 );
33
34 dispData[,"Plate.Number"] <-
35 as.factor(dispData[,"Plate.Number"]);
36 dispData[,"Combination.ID"] <-
37 as.integer(dispData[,"Combination.ID"]);
38
39 rfs = list();
40 #for $raw_assay_file in $input_data.assay_raw
41
42 rfs = append(
43 rfs,
44 metascreen::readRAWData(
45 .readfrom = "$raw_assay_file.element_identifier",
46 .format = "$input_data.assay_format"
47 )
48 );
49 #end for
50
51 names(rfs) <- stringr::str_replace(names(rfs),".csv","");
52
53 clData <- metascreen::consolidateData(
54 dispensingData = dispData,
55 rawMeasurements = rfs,
56 .barcodeReference = barcode_reference);
57
58
59 df = as.data.frame(clData[["consolidated"]]);
60 readr::write_tsv(
61 df, file="$consolidatedData", col_names=T, quote="none");' 2>&1
62
63 ]]></command>
64 <inputs>
65
66 <section name="input_data" title="User-defined input files - see below for formatting requirements" expanded="true">
67 <param name="barcode_reference" type="data" format="txt" label="Barcode reference (CSV)" multiple="false"/>
68 <param name="dispensing_data" type="data" format="txt" label="Dispensing data (TSV)" multiple="false"/>
69 <param name="assay_raw" type="data" format="txt" label="Raw assay measurement data (CSV)" multiple="true"/>
70 <!--param name="convert_platemap_format" type="boolean" label="Convert platemap to a source plate format" truevalue="T" falsevalue="F" checked="false"/-->
71 <param name="assay_format" type="select" label="Assay measurement format" display="radio" multiple="false">
72 <option value="EnVision">EnVision</option>
73 <option value="raw">raw</option>
74 <option value="VICTOR">VICTOR</option>
75 </param>
76 </section>
77
78 </inputs>
79 <outputs>
80 <data format="txt" name="consolidatedData" label="consolidatedData - tsv"/>
81 </outputs>
82
83
84 <help><![CDATA[
85 .. class:: infomark
86
87 Limitations etc:
88
89 -----
90
91 **Dataset formats**
92
93 The input datasets are in text_ (CSV/TSV) format format. The output dataset is also in text_ (TSV) formats.
94
95 .. _text: ${static_path}/formatHelp.html#text
96
97 Specific input file requirements:
98
99 - **List of raw assay measurements** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
100
101 TODO: Briefly describe requirements for *raw* and other available formats for raw assay measurements (EnVision, VICTOR)
102
103 - **Plate barcode reference.** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
104
105 Provides the sample names used in the drug screen and the corresponding plate id and set
106 Format: ['PlateID', 'Set', 'Number','Sample].
107 An example is shown with https://raw.githubusercontent.com/Enserink-lab/screenwerk/main/inst/extdata/library/platebarcode.csv
108
109 - **Dispensing data** - TSV (output from *metascreen: pre-experimental* module)
110
111 -----
112
113 **What it does**
114
115 The intention of the *post-experimental* module of metascreen is to consolidate the raw assay
116 measurements and the dispensing data (the latter produced as output by the *pre-experimental* module
117 of metascreen). The module will build a final reference data set, to be used for
118 any downstream analysis of the drug sensitivity screen. A barcode reference list with the names of
119 the samples used in the drug screen is necessary so that these can be associated to the
120 corresponding plate id and set.
121
122 ]]>
123 </help>
124 <citations>
125 <!-- Example of annotating a citation using a DOI. -->
126 <citation type="doi">10.1093/bioinformatics/btac840</citation>
127 <!-- Example of annotating a citation using a BibTex entry. -->
128 </citations>
129 </tool>