Mercurial > repos > sigven > metascreen_pre_experimental
comparison metascreenPre.xml @ 6:f6e6b6914b48 draft
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author | sigven |
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date | Wed, 21 Dec 2022 23:22:27 +0000 |
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5:e9fcb14b0065 | 6:f6e6b6914b48 |
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1 <tool id="metascreenPre" name="metascreen: pre-experimental" version="0.2.6"> | |
2 <description>Setup 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 ln -f -s $input_data.list_of_drugs "$input_data.list_of_drugs.element_identifier" && | |
8 #set drugs_csv = './' + str($input_data.list_of_drugs.element_identifier) | |
9 | |
10 ln -f -s $input_data.list_of_volumes "$input_data.list_of_volumes.element_identifier" && | |
11 #set volumes_csv = './' + str($input_data.list_of_volumes.element_identifier) | |
12 | |
13 ln -f -s $input_data.list_of_doses "$input_data.list_of_doses.element_identifier" && | |
14 #set doses_csv = './' + str($input_data.list_of_doses.element_identifier) | |
15 | |
16 ln -f -s $input_data.list_of_ctrls "$input_data.list_of_ctrls.element_identifier" && | |
17 #set ctrls_csv = './' + str($input_data.list_of_ctrls.element_identifier) | |
18 | |
19 ln -f -s $input_data.list_of_stock_cons "$input_data.list_of_stock_cons.element_identifier" && | |
20 #set stock_cons_csv = './' + str($input_data.list_of_stock_cons.element_identifier) | |
21 | |
22 #for $pmap in $input_data.platemaps | |
23 ln -f -s '$pmap' '$pmap.element_identifier'; | |
24 #end for | |
25 | |
26 | |
27 #set excluded_well_ids_file = '' | |
28 #if $dispensing_options.well_exclusion.exclude_wells | |
29 echo 'DUMMY_WELL' > excl_well_ids.csv && | |
30 echo $dispensing_options.well_exclusion.well_ids | sed 's/__cn__/\n/g' >> excl_well_ids.csv && | |
31 #set excluded_well_ids_file = './excl_well_ids.csv' | |
32 #end if | |
33 | |
34 R -e 'suppressPackageStartupMessages(library(metascreen)); | |
35 | |
36 custom_excluded_wells = NULL; | |
37 #if $excluded_well_ids_file | |
38 custom_excluded_wells = readr::read_csv( | |
39 "$excluded_well_ids_file", show_col_types = F); | |
40 custom_excluded_wells = custom_excluded_wells[[1]]; | |
41 #end if | |
42 | |
43 list_of_drugs_raw <- read.csv( | |
44 file = "$drugs_csv", | |
45 check.names = FALSE, | |
46 na.strings = "", | |
47 dec = ".", encoding = "UTF-8"); | |
48 list_of_volumes_raw <- read.csv( | |
49 file = "$volumes_csv", | |
50 check.names = FALSE, | |
51 na.strings = "", | |
52 dec = ".", encoding = "UTF-8"); | |
53 list_of_doses_raw <- read.csv( | |
54 file = "$doses_csv", | |
55 check.names = FALSE, | |
56 na.strings = "", | |
57 dec = ".", encoding = "UTF-8"); | |
58 list_of_controls_raw <- read.csv( | |
59 file = "$ctrls_csv", | |
60 check.names = FALSE, | |
61 na.strings = "", | |
62 dec = ".", encoding = "UTF-8"); | |
63 list_of_stock_cons_raw <- read.csv( | |
64 file = "$stock_cons_csv", | |
65 check.names = FALSE, | |
66 na.strings = "", | |
67 dec = ".", encoding = "UTF-8"); | |
68 | |
69 listofDoses <- | |
70 metascreen::generateListofDoses( | |
71 list_of_doses_raw, | |
72 .dropCol = TRUE); | |
73 | |
74 | |
75 sourcePlate = data.frame(); | |
76 #for $pmap in $input_data.platemaps | |
77 | |
78 sourcePlate = dplyr::bind_rows( | |
79 sourcePlate, | |
80 metascreen::importPlateMap( | |
81 "$pmap.element_identifier", | |
82 .fileFormat = "PlateMap", | |
83 .sourcePlateConv = TRUE)); | |
84 #end for | |
85 | |
86 | |
87 | |
88 combine_doses = c(1:min(unique(table(listofDoses[,"Drug"])))); | |
89 exclude_outer_wells = FALSE; | |
90 | |
91 #if $dispensing_options.well_exclusion.exclude_wells | |
92 exclude_outer_wells = $dispensing_options.well_exclusion.outer_wells; | |
93 #end if | |
94 | |
95 #if $combination_options.combo_design.type_combination == "all" | |
96 #if $combination_options.combo_design.inner_dosing | |
97 combine_doses = c(2:(min(unique(table(listofDoses[,"Drug"])))-1)); | |
98 #end if | |
99 #end if | |
100 | |
101 add_untreated = NULL; | |
102 #if $dispensing_options.add_untreated.untreated | |
103 add_untreated = list( | |
104 name = "$dispensing_options.add_untreated.untreated_name", | |
105 replicates = $dispensing_options.add_untreated.untreated_replicates); | |
106 #end if | |
107 | |
108 | |
109 listofExWells <- | |
110 metascreen::excludeWells( | |
111 plateType = $input_data.plateformat, | |
112 wells = custom_excluded_wells, | |
113 outer.wells = exclude_outer_wells); | |
114 | |
115 | |
116 listofCombinations <- | |
117 metascreen::combineDrugs( | |
118 listofDoses, | |
119 .combineDoses = combine_doses, | |
120 .noReplicates = $combination_options.num_replicates, | |
121 .drugRepAttrib = "$combination_options.combo_design.type_combination"); | |
122 | |
123 | |
124 dispensingData <- | |
125 metascreen::generateDispensingData( | |
126 listofCombinations, | |
127 list_of_drugs_raw, | |
128 listofDoses, | |
129 list_of_volumes_raw, | |
130 list_of_controls_raw, | |
131 list_of_stock_cons_raw, | |
132 sourcePlate, | |
133 listofExWells, | |
134 .ctrlReplicates = $dispensing_options.num_control_replicates, | |
135 .addUntreated = add_untreated, | |
136 .finalWellVolume = $dispensing_options.well_volume, | |
137 .plateFormat = $input_data.plateformat, | |
138 .destinationPlateID = "$dispensing_options.dest_plate_ID", | |
139 .randomizeDispensing = $dispensing_options.randomise_dispensing, | |
140 .probeDispensing = $dispensing_options.probe_dispensing); | |
141 | |
142 | |
143 df = as.data.frame(dispensingData[["output"]]); | |
144 readr::write_tsv(listofCombinations,file="$doseComb",col_names=T, quote="none"); | |
145 readr::write_tsv(df,file="$dispensingDF", col_names = T, quote = "none");' 2>&1 | |
146 | |
147 ]]></command> | |
148 <inputs> | |
149 | |
150 <section name="input_data" title="User-defined input files - see below for strict formatting requirements" expanded="true"> | |
151 <param name="list_of_doses" type="data" format="txt" label="List of drug doses (CSV)" multiple="false"/> | |
152 <param name="list_of_drugs" type="data" format="txt" label="List of drugs (CSV)" multiple="false"/> | |
153 <param name="list_of_volumes" type="data" format="txt" label="List of volumes (CSV)" multiple="false"/> | |
154 <param name="list_of_ctrls" type="data" format="txt" label="List of controls (CSV)" multiple="false"/> | |
155 <param name="list_of_stock_cons" type="data" format="txt" label="List of stock concentrations (CSV)" multiple="false"/> | |
156 <param name="platemaps" type="data" format="xml" label="PlateMap file (XML)" multiple="true"/> | |
157 <!--param name="convert_platemap_format" type="boolean" label="Convert platemap to a source plate format" truevalue="T" falsevalue="F" checked="false"/--> | |
158 <param name="plateformat" type="select" label="Plate format" display="radio" multiple="false"> | |
159 <option value="6">6</option> | |
160 <option value="12">12</option> | |
161 <option value="24">24</option> | |
162 <option value="48">48</option> | |
163 <option value="96">96</option> | |
164 <option value="384">384</option> | |
165 <option value="1536">1536</option> | |
166 </param> | |
167 </section> | |
168 | |
169 <section name="combination_options" title="Options - drug combination design" expanded="true"> | |
170 <conditional name="combo_design"> | |
171 <param name="type_combination" type="select" display="radio" multiple="false" label="Type of dose combinations"> | |
172 <option value="all">All - both single treatments and combination treatments</option> | |
173 <option value="single">Single - only single treatments</option> | |
174 </param> | |
175 <when value="all"> | |
176 <param name="inner_dosing" type="boolean" label="Exclude lowest and highest dose (inner dosing only)" truevalue="T" falsevalue="F" checked="false"/> | |
177 </when> | |
178 </conditional> | |
179 <param type="integer" name="num_replicates" label="Number of replicates for each dose combination" value="3" min="1" max="20"/> | |
180 </section> | |
181 <section name="dispensing_options" title="Options - dispensing layout" expanded="true"> | |
182 <!--param name="out_dir" type="text" size="25" label="Dispensing files" value="dispFiles" /--> | |
183 <conditional name="well_exclusion"> | |
184 <param name="exclude_wells" type="boolean" label="Exclusion of wells" truevalue="T" falsevalue="F" checked="false"/> | |
185 <when value="T"> | |
186 <param name="well_ids" type="text" label="Custom set of well identifiers to exclude (one per line):" area="true"/> | |
187 <param name="outer_wells" type="boolean" label="Exclude all outer wells" truevalue="T" falsevalue="F" checked="true"/> | |
188 </when> | |
189 </conditional> | |
190 <param name="num_control_replicates" type="integer" label="Number of control replicates" value="3" min="1" max="10"/> | |
191 <param name="well_volume" type="integer" label="Final well volume" value="5" min="1" max="500"/> | |
192 <param name="randomise_dispensing" type="boolean" label="Randomise dispensing" truevalue="T" falsevalue="F" checked="true"/> | |
193 <param name="probe_dispensing" type="boolean" label="Probe dispensing" truevalue="T" falsevalue="F" checked="false"/> | |
194 <param name="dest_plate_ID" type="text" value="PLATE_012" label="A unique destination plate ID - for destination plate barcode"/> | |
195 <conditional name="add_untreated"> | |
196 <param name="untreated" type="boolean" label="Add untreated" truevalue="T" falsevalue="F" checked="true"/> | |
197 <when value="T"> | |
198 <param name="untreated_name" type="text" label="Identifier (name) for untreated" value="Untreated"/> | |
199 <param name="untreated_replicates" type="integer" label="Number of untreated replicates" value="5" min="1" max="500"/> | |
200 </when> | |
201 </conditional> | |
202 | |
203 </section> | |
204 </inputs> | |
205 <outputs> | |
206 <!--data format="xlsx" name="output_xlsx" label="crisprFPA - xlsx"/--> | |
207 <data format="txt" name="doseComb" label="doseCombinations - tsv"/> | |
208 <data format="txt" name="dispensingDF" label="dispensingData - tsv"/> | |
209 <!--data format="rdata" name="dispensingRDA" label="dispensingData - rda"/--> | |
210 | |
211 <!--collection type="list" name="dispensingFiles" label="dispensingFiles"> | |
212 <discover_datasets pattern=".csv" format="txt" directory="dispFiles" /> | |
213 </collection--> | |
214 </outputs> | |
215 | |
216 | |
217 <help><![CDATA[ | |
218 .. class:: infomark | |
219 | |
220 Limitations etc: | |
221 | |
222 ----- | |
223 | |
224 **Dataset formats** | |
225 | |
226 The input datasets are in text_ (CSV) format and in XML format. The output datasets are also in text_ formats. | |
227 | |
228 .. _text: ${static_path}/formatHelp.html#text | |
229 | |
230 Specific input file requirements: | |
231 | |
232 - **List of drug doses** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file | |
233 | |
234 Provides a list of all the doses for each drug used in | |
235 a drug sensitivity screen. The list needs to include a column with the drug number, | |
236 drug name, one or multiple columns for the doses, and a column with the unit. | |
237 ['Number', 'Drug', '6th Dose', ..., '1st Dose', 'Unit']. | |
238 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofdoses.csv | |
239 | |
240 - **List of drugs.** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file | |
241 | |
242 Provides a list of drugs used in the drug screen. The list | |
243 needs to include a column with a unique drug number / id for each drug, the | |
244 drug name and the CAS number. ['ID', 'NAME', 'CAS_NUMBER']. For custom | |
245 compunds without CAS number, include column, but leave field empty. | |
246 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofdrugs.csv | |
247 | |
248 - **List of stock concentrations.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file | |
249 | |
250 Provides a list of the stock concentrations | |
251 for each drug used in the drug screen. If the stock concentrations are not | |
252 known, use the highest dose. The list needs to include column with the unique | |
253 drug number / id, the drug name, the stock concentration and the concentration unit. | |
254 ['NUMBER', 'NAME', 'CONCENTRATION', 'UNIT']. | |
255 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofstockconcentrations.csv | |
256 | |
257 - **List of controls.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file | |
258 | |
259 Provides the controls to be used in a drug | |
260 screen. The list needs to include a column with the name, CAS number, | |
261 dose, unit, the source plate from which the control is dispensed from and the | |
262 volume. ['NAME', 'CAS_NUMBER', 'DOSE', 'UNIT', 'SOURCE_PLATE', 'VOLUME']. | |
263 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofctrls.csv | |
264 | |
265 - **List of drug volumes.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file | |
266 | |
267 Provides the volumes for each drug that | |
268 have been or will be dispensed. The list follows the same format as the | |
269 list of drug doses. The list needs to include a column with the drug number, | |
270 drug name, one or multiple columns with doses, and a column with the unit. | |
271 ['Number', 'Drug', 'Vol 6th Dose', ..., 'Vol 1st Dose', 'Unit']. | |
272 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofvolumes.csv | |
273 | |
274 | |
275 - **plateMap** - XML file (s) | |
276 | |
277 One or more plate map files with the contents (usually compounds/drugs) of the | |
278 source plate from which drugs are dispensed from. Plate maps can currently be imported | |
279 using .PlateMap (XML files) provided by the IncuCyte® Plate Map Editor. **IMPORTANT: when uploading | |
280 PlateMap files to Galaxy, please make sure you denote file 'Type' as XML.** | |
281 | |
282 An example is shown with https://github.com/Enserink-lab/metascreen/blob/main/inst/extdata/library/C008.PlateMap | |
283 | |
284 ----- | |
285 | |
286 **What it does** | |
287 | |
288 The *pre-experimental* modules of metascreen is intended to serve the following purposes: | |
289 | |
290 set up drug combination screens by (a) generating drug combinations from a list of drugs, and | |
291 (b) distributing those drug combinations across a number of experimental plates, | |
292 (c) generating instructions for dispensing robots for the creation of those | |
293 experimental plates. | |
294 | |
295 | |
296 | |
297 | |
298 | |
299 | |
300 ]]> | |
301 </help> | |
302 | |
303 </tool> |