annotate metascreen.xml @ 4:22251a4b8f8f draft

Uploaded
author sigven
date Fri, 11 Nov 2022 14:49:08 +0000
parents 2315c8ea7d2f
children e9fcb14b0065
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
22251a4b8f8f Uploaded
sigven
parents: 3
diff changeset
1 <tool id="metascreenPre" name="mscreen: pre-experimental" version="0.2.2">
2
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
2 <description>Pre-experimental setup of drug combination screens</description>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
3 <requirements>
3
2315c8ea7d2f Uploaded
sigven
parents: 2
diff changeset
4 <container type="docker">sigven/metascreen:0.2.0</container>
2
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
5 </requirements>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
6 <command detect_errors="aggressive"><![CDATA[
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
7 ln -s $input_data.list_of_drugs "$input_data.list_of_drugs.element_identifier" &&
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
8 #set drugs_csv = './' + str($input_data.list_of_drugs.element_identifier)
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
9
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
10 ln -s $input_data.list_of_volumes "$input_data.list_of_volumes.element_identifier" &&
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
11 #set volumes_csv = './' + str($input_data.list_of_volumes.element_identifier)
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
12
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
13 ln -s $input_data.list_of_doses "$input_data.list_of_doses.element_identifier" &&
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
14 #set doses_csv = './' + str($input_data.list_of_doses.element_identifier)
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
15
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
16 ln -s $input_data.list_of_ctrls "$input_data.list_of_ctrls.element_identifier" &&
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
17 #set ctrls_csv = './' + str($input_data.list_of_ctrls.element_identifier)
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
18
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
19 ln -s $input_data.list_of_stock_cons "$input_data.list_of_stock_cons.element_identifier" &&
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
20 #set stock_cons_csv = './' + str($input_data.list_of_stock_cons.element_identifier)
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
21
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
22 #for $pmap in $input_data.platemaps
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
23 ln -s '$pmap' '$pmap.element_identifier';
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
24 #end for
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
25
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
26
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
27 #set excluded_well_ids_file = ''
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
28 #if $dispensing_options.well_exclusion.exclude_wells
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
29 echo $dispensing_options.well_exclusion.well_ids | sed 's/__cn__/\n/g' > excl_well_ids.csv &&
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
30 #set excluded_well_ids_file = './excl_well_ids.csv'
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
31 #end if
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
32
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
33 R -e 'suppressPackageStartupMessages(library(metascreen));
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
34
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
35 custom_excluded_wells = NULL;
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
36 #if $excluded_well_ids_file
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
37 custom_excluded_wells = read.csv(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
38 "$excluded_well_ids_file", stringsAsFactors = F, header = F);
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
39 custom_excluded_wells = custom_excluded_wells[[1]];
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
40 #end if
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
41
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
42 list_of_drugs_raw <- read.csv(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
43 file = "$drugs_csv",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
44 check.names = FALSE,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
45 na.strings = "",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
46 dec = ".", encoding = "UTF-8");
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
47 list_of_volumes_raw <- read.csv(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
48 file = "$volumes_csv",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
49 check.names = FALSE,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
50 na.strings = "",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
51 dec = ".", encoding = "UTF-8");
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
52 list_of_doses_raw <- read.csv(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
53 file = "$doses_csv",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
54 check.names = FALSE,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
55 na.strings = "",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
56 dec = ".", encoding = "UTF-8");
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
57 list_of_controls_raw <- read.csv(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
58 file = "$ctrls_csv",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
59 check.names = FALSE,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
60 na.strings = "",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
61 dec = ".", encoding = "UTF-8");
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
62 list_of_stock_cons_raw <- read.csv(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
63 file = "$stock_cons_csv",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
64 check.names = FALSE,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
65 na.strings = "",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
66 dec = ".", encoding = "UTF-8");
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
67
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
68 listofDoses <-
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
69 metascreen::generateListofDoses(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
70 list_of_doses_raw,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
71 .dropCol = TRUE);
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
72
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
73
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
74 sourcePlate = data.frame();
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
75 #for $pmap in $input_data.platemaps
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
76
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
77 sourcePlate = dplyr::bind_rows(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
78 sourcePlate,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
79 metascreen::importPlateMap(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
80 "$pmap.element_identifier",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
81 .fileFormat = "PlateMap",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
82 .sourcePlateConv = $input_data.convert_platemap_format
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
83 )
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
84 );
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
85 #end for
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
86
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
87 combine_doses = c(1:min(unique(table(listofDoses[,"Drug"]))));
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
88 exclude_outer_wells = FALSE;
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
89
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
90 #if $dispensing_options.well_exclusion.exclude_wells
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
91 exclude_outer_wells = $dispensing_options.well_exclusion.outer_wells;
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
92 #end if
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
93
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
94 #if $combination_options.combo_design.type_combination == "all"
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
95 #if $combination_options.combo_design.inner_dosing
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
96 combine_doses = c(2:(min(unique(table(listofDoses[,"Drug"])))-1));
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
97 #end if
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
98 #end if
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
99
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
100 add_untreated = NULL;
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
101 #if $dispensing_options.add_untreated.untreated
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
102 add_untreated = list(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
103 name = "$dispensing_options.add_untreated.untreated_name",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
104 replicates = $dispensing_options.add_untreated.untreated_replicates);
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
105 #end if
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
106
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
107
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
108 listofExWells <-
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
109 metascreen::excludeWells(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
110 plateType = $input_data.plateformat,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
111 wells = custom_excluded_wells,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
112 outer.wells = exclude_outer_wells);
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
113
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
114
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
115 listofCombinations <-
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
116 metascreen::combineDrugs(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
117 listofDoses,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
118 .combineDoses = combine_doses,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
119 .noReplicates = $combination_options.num_replicates,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
120 .drugRepAttrib = "$combination_options.combo_design.type_combination");
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
121
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
122
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
123 dispensingData <-
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
124 metascreen::generateDispensingData(
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
125 listofCombinations,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
126 list_of_drugs_raw,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
127 listofDoses,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
128 list_of_volumes_raw,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
129 list_of_controls_raw,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
130 list_of_stock_cons_raw,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
131 sourcePlate,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
132 listofExWells,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
133 .ctrlReplicates = $dispensing_options.num_control_replicates,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
134 .addUntreated = add_untreated,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
135 .finalWellVolume = $dispensing_options.well_volume,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
136 .plateFormat = $input_data.plateformat,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
137 .destinationPlateID = "$dispensing_options.dest_plate_ID",
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
138 .randomizeDispensing = $dispensing_options.randomise_dispensing,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
139 .probeDispensing = $dispensing_options.probe_dispensing);
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
140
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
141 df = as.data.frame(dispensingData[["output"]]);
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
142 readr::write_tsv(listofCombinations,file="$doseComb",col_names=T, quote="none");
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
143 readr::write_tsv(df,file="$dispensingDF", col_names = T, quote = "none");' 2>&1
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
144
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
145 ]]></command>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
146 <inputs>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
147
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
148 <section name="input_data" title="User-defined input files - see below for strict formatting requirements" expanded="true">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
149 <param name="list_of_doses" type="data" format="txt" label="List of drug doses (CSV)" multiple="false"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
150 <param name="list_of_drugs" type="data" format="txt" label="List of drugs (CSV)" multiple="false"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
151 <param name="list_of_volumes" type="data" format="txt" label="List of volumes (CSV)" multiple="false"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
152 <param name="list_of_ctrls" type="data" format="txt" label="List of controls (CSV)" multiple="false"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
153 <param name="list_of_stock_cons" type="data" format="txt" label="List of stock concentrations (CSV)" multiple="false"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
154 <param name="platemaps" type="data" format="xml" label="PlateMap file (XML)" multiple="true"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
155 <param name="convert_platemap_format" type="boolean" label="Convert platemap to a source plate format" truevalue="T" falsevalue="F" checked="false"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
156 <param name="plateformat" type="select" label="Plate format" display="radio" multiple="false">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
157 <option value="6">6</option>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
158 <option value="12">12</option>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
159 <option value="24">24</option>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
160 <option value="48">48</option>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
161 <option value="96">96</option>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
162 <option value="384">384</option>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
163 <option value="1536">1536</option>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
164 </param>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
165 </section>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
166
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
167 <section name="combination_options" title="Options - drug combination design" expanded="true">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
168 <conditional name="combo_design">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
169 <param name="type_combination" type="select" display="radio" multiple="false" label="Type of dose combinations">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
170 <option value="all">All - both single treatments and combination treatments</option>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
171 <option value="single">Single - only single treatments</option>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
172 </param>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
173 <when value="all">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
174 <param name="inner_dosing" type="boolean" label="Exclude lowest and highest dose (inner dosing only)" truevalue="T" falsevalue="F" checked="false"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
175 </when>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
176 </conditional>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
177 <param type="integer" name="num_replicates" label="Number of replicates for each dose combination" value="3" min="1" max="20"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
178 </section>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
179 <section name="dispensing_options" title="Options - dispensing layout" expanded="true">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
180 <conditional name="well_exclusion">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
181 <param name="exclude_wells" type="boolean" label="Exclusion of wells" truevalue="T" falsevalue="F" checked="false"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
182 <when value="T">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
183 <param name="well_ids" type="text" label="Custom set of well identifiers to exclude (one per line):" area="true"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
184 <param name="outer_wells" type="boolean" label="Exclude all outer wells" truevalue="T" falsevalue="F" checked="true"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
185 </when>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
186 </conditional>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
187 <param name="num_control_replicates" type="integer" label="Number of control replicates" value="5" min="1" max="10"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
188 <param name="well_volume" type="integer" label="Final well volume" value="10" min="1" max="500"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
189 <param name="randomise_dispensing" type="boolean" label="Randomise dispensing" truevalue="T" falsevalue="F" checked="true"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
190 <param name="probe_dispensing" type="boolean" label="Probe dispensing" truevalue="T" falsevalue="F" checked="false"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
191 <param name="dest_plate_ID" type="text" value="PLATE_012" label="A unique destination plate ID - for destination plate barcode"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
192 <conditional name="add_untreated">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
193 <param name="untreated" type="boolean" label="Add untreated" truevalue="T" falsevalue="F" checked="true"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
194 <when value="T">
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
195 <param name="untreated_name" type="text" label="Identifier (name) for untreated" value="Untreated"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
196 <param name="untreated_replicates" type="integer" label="Number of untreated replicates" value="5" min="1" max="500"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
197 </when>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
198 </conditional>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
199
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
200 </section>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
201 </inputs>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
202 <outputs>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
203 <!--data format="xlsx" name="output_xlsx" label="crisprFPA - xlsx"/-->
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
204 <data format="txt" name="doseComb" label="doseCombinations - tsv"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
205 <data format="txt" name="dispensingDF" label="dispensingData - tsv"/>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
206 </outputs>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
207
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
208
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
209 <help><![CDATA[
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
210 .. class:: infomark
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
211
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
212 Limitations etc:
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
213
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
214 -----
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
215
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
216 **Dataset formats**
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
217
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
218 The input datasets are in text_ (CSV) format and in XML format. The output datasets are also in text_ formats.
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
219
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
220 .. _text: ${static_path}/formatHelp.html#text
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
221
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
222 Specific input file requirements:
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
223
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
224 - **List of drug doses** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
225
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
226 Provides a list of all the doses for each drug used in
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
227 a drug sensitivity screen. The list needs to include a column with the drug number,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
228 drug name, one or multiple columns for the doses, and a column with the unit.
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
229 ['Number', 'Drug', '6th Dose', ..., '1st Dose', 'Unit'].
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
230 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofdoses.csv
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
231
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
232 - **List of drugs.** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
233
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
234 Provides a list of drugs used in the drug screen. The list
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
235 needs to include a column with a unique drug number / id for each drug, the
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
236 drug name and the CAS number. ['ID', 'NAME', 'CAS_NUMBER']. For custom
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
237 compunds without CAS number, include column, but leave field empty.
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
238 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofdrugs.csv
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
239
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
240 - **List of stock concentrations.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
241
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
242 Provides a list of the stock concentrations
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
243 for each drug used in the drug screen. If the stock concentrations are not
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
244 known, use the highest dose. The list needs to include column with the unique
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
245 drug number / id, the drug name, the stock concentration and the concentration unit.
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
246 ['NUMBER', 'NAME', 'CONCENTRATION', 'UNIT'].
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
247 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofstockconcentrations.csv
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
248
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
249 - **List of controls.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
250
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
251 Provides the controls to be used in a drug
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
252 screen. The list needs to include a column with the name, CAS number,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
253 dose, unit, the source plate from which the control is dispensed from and the
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
254 volume. ['NAME', 'CAS_NUMBER', 'DOSE', 'UNIT', 'SOURCE_PLATE', 'VOLUME'].
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
255 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofctrls.csv
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
256
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
257 - **List of drug volumes.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
258
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
259 Provides the volumes for each drug that
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
260 have been or will be dispensed. The list follows the same format as the
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
261 list of drug doses. The list needs to include a column with the drug number,
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
262 drug name, one or multiple columns with doses, and a column with the unit.
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
263 ['Number', 'Drug', 'Vol 6th Dose', ..., 'Vol 1st Dose', 'Unit'].
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
264 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofvolumes.csv
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
265
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
266
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
267 - **plateMap** - XML file (s)
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
268
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
269 One or more plate map files with the contents (usually compounds/drugs) of the
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
270 source plate from which drugs are dispensed from. Plate maps can currently be imported
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
271 using .PlateMap (XML files) provided by the IncuCyte® Plate Map Editor. **IMPORTANT: when uploading
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
272 PlateMap files to Galaxy, please make sure you denote file 'Type' as XML.**
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
273
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
274 An example is shown with https://github.com/Enserink-lab/metascreen/blob/main/inst/extdata/library/C008.PlateMap
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
275
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
276 -----
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
277
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
278 **What it does**
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
279
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
280 The *pre-experimental* modules of metascreen is intended to serve the following purposes:
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
281
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
282 allowing to set-up a drug combination screens by (a) generating drug combinations from a list of drugs and
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
283 (b) distributing those drug combinations across a number of experimental plates. (c) generating instructions
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
284 for dispensing robots for the creation of those experimental plates.
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
285
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
286
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
287
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
288
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
289
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
290
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
291 ]]>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
292 </help>
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
293
80e9dd6942c0 Uploaded
sigven
parents:
diff changeset
294 </tool>