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comparison metascreen.xml @ 0:600a6823fcd4 draft

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author sigven
date Thu, 10 Nov 2022 20:47:57 +0000
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1 <tool id="metascreenPre" name="mscreen: pre-experimental" version="0.2.0">
2 <description>Pre-experimental setup of drug combination screens</description>
3 <command detect_errors="aggressive"><![CDATA[
4 ln -s $input_data.list_of_drugs "$input_data.list_of_drugs.element_identifier" &&
5 #set drugs_csv = './' + str($input_data.list_of_drugs.element_identifier)
6
7 ln -s $input_data.list_of_volumes "$input_data.list_of_volumes.element_identifier" &&
8 #set volumes_csv = './' + str($input_data.list_of_volumes.element_identifier)
9
10 ln -s $input_data.list_of_doses "$input_data.list_of_doses.element_identifier" &&
11 #set doses_csv = './' + str($input_data.list_of_doses.element_identifier)
12
13 ln -s $input_data.list_of_ctrls "$input_data.list_of_ctrls.element_identifier" &&
14 #set ctrls_csv = './' + str($input_data.list_of_ctrls.element_identifier)
15
16 ln -s $input_data.list_of_stock_cons "$input_data.list_of_stock_cons.element_identifier" &&
17 #set stock_cons_csv = './' + str($input_data.list_of_stock_cons.element_identifier)
18
19 #for $pmap in $input_data.platemaps
20 ln -s '$pmap' '$pmap.element_identifier';
21 #end for
22
23
24 #set excluded_well_ids_file = ''
25 #if $dispensing_options.well_exclusion.exclude_wells
26 echo $dispensing_options.well_exclusion.well_ids | sed 's/__cn__/\n/g' > excl_well_ids.csv &&
27 #set excluded_well_ids_file = './excl_well_ids.csv'
28 #end if
29
30 R -e 'suppressPackageStartupMessages(library(metascreen));
31
32 custom_excluded_wells = NULL;
33 #if $excluded_well_ids_file
34 custom_excluded_wells = read.csv(
35 "$excluded_well_ids_file", stringsAsFactors = F, header = F);
36 custom_excluded_wells = custom_excluded_wells[[1]];
37 #end if
38
39 list_of_drugs_raw <- read.csv(
40 file = "$drugs_csv",
41 check.names = FALSE,
42 na.strings = "",
43 dec = ".", encoding = "UTF-8");
44 list_of_volumes_raw <- read.csv(
45 file = "$volumes_csv",
46 check.names = FALSE,
47 na.strings = "",
48 dec = ".", encoding = "UTF-8");
49 list_of_doses_raw <- read.csv(
50 file = "$doses_csv",
51 check.names = FALSE,
52 na.strings = "",
53 dec = ".", encoding = "UTF-8");
54 list_of_controls_raw <- read.csv(
55 file = "$ctrls_csv",
56 check.names = FALSE,
57 na.strings = "",
58 dec = ".", encoding = "UTF-8");
59 list_of_stock_cons_raw <- read.csv(
60 file = "$stock_cons_csv",
61 check.names = FALSE,
62 na.strings = "",
63 dec = ".", encoding = "UTF-8");
64
65 listofDoses <-
66 metascreen::generateListofDoses(
67 list_of_doses_raw,
68 .dropCol = TRUE);
69
70
71 sourcePlate = data.frame();
72 #for $pmap in $input_data.platemaps
73
74 sourcePlate = dplyr::bind_rows(
75 sourcePlate,
76 metascreen::importPlateMap(
77 "$pmap.element_identifier",
78 .fileFormat = "PlateMap",
79 galaxy = TRUE,
80 .sourcePlateConv = $input_data.convert_platemap_format
81 )
82 );
83 #end for
84
85 combine_doses = c(1:min(unique(table(listofDoses[,"Drug"]))));
86 exclude_outer_wells = FALSE;
87
88 #if $dispensing_options.well_exclusion.exclude_wells
89 exclude_outer_wells = $dispensing_options.well_exclusion.outer_wells;
90 #end if
91
92 #if $combination_options.combo_design.type_combination == "all"
93 #if $combination_options.combo_design.inner_dosing
94 combine_doses = c(2:(min(unique(table(listofDoses[,"Drug"])))-1));
95 #end if
96 #end if
97
98 add_untreated = NULL;
99 #if $dispensing_options.add_untreated.untreated
100 add_untreated = list(
101 name = "$dispensing_options.add_untreated.untreated_name",
102 replicates = $dispensing_options.add_untreated.untreated_replicates);
103 #end if
104
105
106 listofExWells <-
107 metascreen::excludeWells(
108 plateType = $input_data.plateformat,
109 wells = custom_excluded_wells,
110 outer.wells = exclude_outer_wells);
111
112
113 listofCombinations <-
114 metascreen::combineDrugs(
115 listofDoses,
116 .combineDoses = combine_doses,
117 .noReplicates = $combination_options.num_replicates,
118 .drugRepAttrib = "$combination_options.combo_design.type_combination");
119
120
121 dispensingData <-
122 metascreen::generateDispensingData(
123 listofCombinations,
124 list_of_drugs_raw,
125 listofDoses,
126 list_of_volumes_raw,
127 list_of_controls_raw,
128 list_of_stock_cons_raw,
129 sourcePlate,
130 listofExWells,
131 .ctrlReplicates = $dispensing_options.num_control_replicates,
132 .addUntreated = add_untreated,
133 .finalWellVolume = $dispensing_options.well_volume,
134 .plateFormat = $input_data.plateformat,
135 .destinationPlateID = "$dispensing_options.dest_plate_ID",
136 .randomizeDispensing = $dispensing_options.randomise_dispensing,
137 .probeDispensing = $dispensing_options.probe_dispensing);
138
139 df = as.data.frame(dispensingData[["output"]]);
140 readr::write_tsv(listofCombinations,file="$doseComb",col_names=T, quote="none");
141 readr::write_tsv(df,file="$dispensingDF", col_names = T, quote = "none");' 2>&1
142
143 ]]></command>
144 <inputs>
145
146 <section name="input_data" title="User-defined input files - see below for strict formatting requirements" expanded="true">
147 <param name="list_of_doses" type="data" format="txt" label="List of drug doses (CSV)" multiple="false"/>
148 <param name="list_of_drugs" type="data" format="txt" label="List of drugs (CSV)" multiple="false"/>
149 <param name="list_of_volumes" type="data" format="txt" label="List of volumes (CSV)" multiple="false"/>
150 <param name="list_of_ctrls" type="data" format="txt" label="List of controls (CSV)" multiple="false"/>
151 <param name="list_of_stock_cons" type="data" format="txt" label="List of stock concentrations (CSV)" multiple="false"/>
152 <param name="platemaps" type="data" format="xml" label="PlateMap file (XML)" multiple="true"/>
153 <param name="convert_platemap_format" type="boolean" label="Convert platemap to a source plate format" truevalue="T" falsevalue="F" checked="false"/>
154 <param name="plateformat" type="select" label="Plate format" display="radio" multiple="false">
155 <option value="6">6</option>
156 <option value="12">12</option>
157 <option value="24">24</option>
158 <option value="48">48</option>
159 <option value="96">96</option>
160 <option value="384">384</option>
161 <option value="1536">1536</option>
162 </param>
163 </section>
164
165 <section name="combination_options" title="Options - drug combination design" expanded="true">
166 <conditional name="combo_design">
167 <param name="type_combination" type="select" display="radio" multiple="false" label="Type of dose combinations">
168 <option value="all">All - both single treatments and combination treatments</option>
169 <option value="single">Single - only single treatments</option>
170 </param>
171 <when value="all">
172 <param name="inner_dosing" type="boolean" label="Exclude lowest and highest dose (inner dosing only)" truevalue="T" falsevalue="F" checked="false"/>
173 </when>
174 </conditional>
175 <param type="integer" name="num_replicates" label="Number of replicates for each dose combination" value="3" min="1" max="20"/>
176 </section>
177 <section name="dispensing_options" title="Options - dispensing layout" expanded="true">
178 <conditional name="well_exclusion">
179 <param name="exclude_wells" type="boolean" label="Exclusion of wells" truevalue="T" falsevalue="F" checked="false"/>
180 <when value="T">
181 <param name="well_ids" type="text" label="Custom set of well identifiers to exclude (one per line):" area="true"/>
182 <param name="outer_wells" type="boolean" label="Exclude all outer wells" truevalue="T" falsevalue="F" checked="true"/>
183 </when>
184 </conditional>
185 <param name="num_control_replicates" type="integer" label="Number of control replicates" value="5" min="1" max="10"/>
186 <param name="well_volume" type="integer" label="Final well volume" value="10" min="1" max="500"/>
187 <param name="randomise_dispensing" type="boolean" label="Randomise dispensing" truevalue="T" falsevalue="F" checked="true"/>
188 <param name="probe_dispensing" type="boolean" label="Probe dispensing" truevalue="T" falsevalue="F" checked="false"/>
189 <param name="dest_plate_ID" type="text" value="PLATE_012" label="A unique destination plate ID - for destination plate barcode"/>
190 <conditional name="add_untreated">
191 <param name="untreated" type="boolean" label="Add untreated" truevalue="T" falsevalue="F" checked="true"/>
192 <when value="T">
193 <param name="untreated_name" type="text" label="Identifier (name) for untreated" value="Untreated"/>
194 <param name="untreated_replicates" type="integer" label="Number of untreated replicates" value="5" min="1" max="500"/>
195 </when>
196 </conditional>
197
198 </section>
199 </inputs>
200 <outputs>
201 <!--data format="xlsx" name="output_xlsx" label="crisprFPA - xlsx"/-->
202 <data format="txt" name="doseComb" label="doseCombinations - tsv"/>
203 <data format="txt" name="dispensingDF" label="dispensingData - tsv"/>
204 </outputs>
205
206
207 <help><![CDATA[
208 .. class:: infomark
209
210 Limitations etc:
211
212 -----
213
214 **Dataset formats**
215
216 The input datasets are in text_ (CSV) format and in XML format. The output datasets are also in text_ formats.
217
218 .. _text: ${static_path}/formatHelp.html#text
219
220 Specific input file requirements:
221
222 - **List of drug doses** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
223
224 Provides a list of all the doses for each drug used in
225 a drug sensitivity screen. The list needs to include a column with the drug number,
226 drug name, one or multiple columns for the doses, and a column with the unit.
227 ['Number', 'Drug', '6th Dose', ..., '1st Dose', 'Unit'].
228 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofdoses.csv
229
230 - **List of drugs.** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
231
232 Provides a list of drugs used in the drug screen. The list
233 needs to include a column with a unique drug number / id for each drug, the
234 drug name and the CAS number. ['ID', 'NAME', 'CAS_NUMBER']. For custom
235 compunds without CAS number, include column, but leave field empty.
236 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofdrugs.csv
237
238 - **List of stock concentrations.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
239
240 Provides a list of the stock concentrations
241 for each drug used in the drug screen. If the stock concentrations are not
242 known, use the highest dose. The list needs to include column with the unique
243 drug number / id, the drug name, the stock concentration and the concentration unit.
244 ['NUMBER', 'NAME', 'CONCENTRATION', 'UNIT'].
245 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofstockconcentrations.csv
246
247 - **List of controls.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
248
249 Provides the controls to be used in a drug
250 screen. The list needs to include a column with the name, CAS number,
251 dose, unit, the source plate from which the control is dispensed from and the
252 volume. ['NAME', 'CAS_NUMBER', 'DOSE', 'UNIT', 'SOURCE_PLATE', 'VOLUME'].
253 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofctrls.csv
254
255 - **List of drug volumes.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
256
257 Provides the volumes for each drug that
258 have been or will be dispensed. The list follows the same format as the
259 list of drug doses. The list needs to include a column with the drug number,
260 drug name, one or multiple columns with doses, and a column with the unit.
261 ['Number', 'Drug', 'Vol 6th Dose', ..., 'Vol 1st Dose', 'Unit'].
262 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofvolumes.csv
263
264
265 - **plateMap** - XML file (s)
266
267 One or more plate map files with the contents (usually compounds/drugs) of the
268 source plate from which drugs are dispensed from. Plate maps can currently be imported
269 using .PlateMap (XML files) provided by the IncuCyte® Plate Map Editor. **IMPORTANT: when uploading
270 PlateMap files to Galaxy, please make sure you denote file 'Type' as XML.**
271
272 An example is shown with https://github.com/Enserink-lab/metascreen/blob/main/inst/extdata/library/C008.PlateMap
273
274 -----
275
276 **What it does**
277
278 The *pre-experimental* modules of metascreen is intended to serve the following purposes:
279
280 allowing to set-up a drug combination screens by (a) generating drug combinations from a list of drugs and
281 (b) distributing those drug combinations across a number of experimental plates. (c) generating instructions
282 for dispensing robots for the creation of those experimental plates.
283
284
285
286
287
288
289 ]]>
290 </help>
291
292 </tool>