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3
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1 <tool id="metascreenPre" name="mscreen: pre-experimental" version="0.2.1">
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2
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2 <description>Pre-experimental setup of drug combination screens</description>
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3 <requirements>
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3
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4 <container type="docker">sigven/metascreen:0.2.0</container>
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2
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7 ln -s $input_data.list_of_drugs "$input_data.list_of_drugs.element_identifier" &&
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8 #set drugs_csv = './' + str($input_data.list_of_drugs.element_identifier)
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9
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10 ln -s $input_data.list_of_volumes "$input_data.list_of_volumes.element_identifier" &&
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11 #set volumes_csv = './' + str($input_data.list_of_volumes.element_identifier)
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12
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13 ln -s $input_data.list_of_doses "$input_data.list_of_doses.element_identifier" &&
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14 #set doses_csv = './' + str($input_data.list_of_doses.element_identifier)
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15
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16 ln -s $input_data.list_of_ctrls "$input_data.list_of_ctrls.element_identifier" &&
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17 #set ctrls_csv = './' + str($input_data.list_of_ctrls.element_identifier)
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18
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19 ln -s $input_data.list_of_stock_cons "$input_data.list_of_stock_cons.element_identifier" &&
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20 #set stock_cons_csv = './' + str($input_data.list_of_stock_cons.element_identifier)
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21
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22 #for $pmap in $input_data.platemaps
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23 ln -s '$pmap' '$pmap.element_identifier';
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24 #end for
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25
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26
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27 #set excluded_well_ids_file = ''
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28 #if $dispensing_options.well_exclusion.exclude_wells
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29 echo $dispensing_options.well_exclusion.well_ids | sed 's/__cn__/\n/g' > excl_well_ids.csv &&
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30 #set excluded_well_ids_file = './excl_well_ids.csv'
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31 #end if
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32
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33 R -e 'suppressPackageStartupMessages(library(metascreen));
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34
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35 custom_excluded_wells = NULL;
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36 #if $excluded_well_ids_file
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37 custom_excluded_wells = read.csv(
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38 "$excluded_well_ids_file", stringsAsFactors = F, header = F);
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39 custom_excluded_wells = custom_excluded_wells[[1]];
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40 #end if
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41
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42 list_of_drugs_raw <- read.csv(
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43 file = "$drugs_csv",
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44 check.names = FALSE,
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45 na.strings = "",
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46 dec = ".", encoding = "UTF-8");
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47 list_of_volumes_raw <- read.csv(
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48 file = "$volumes_csv",
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49 check.names = FALSE,
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50 na.strings = "",
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51 dec = ".", encoding = "UTF-8");
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52 list_of_doses_raw <- read.csv(
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53 file = "$doses_csv",
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54 check.names = FALSE,
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55 na.strings = "",
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56 dec = ".", encoding = "UTF-8");
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57 list_of_controls_raw <- read.csv(
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58 file = "$ctrls_csv",
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59 check.names = FALSE,
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60 na.strings = "",
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61 dec = ".", encoding = "UTF-8");
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62 list_of_stock_cons_raw <- read.csv(
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63 file = "$stock_cons_csv",
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64 check.names = FALSE,
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65 na.strings = "",
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66 dec = ".", encoding = "UTF-8");
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67
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68 listofDoses <-
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69 metascreen::generateListofDoses(
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70 list_of_doses_raw,
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71 .dropCol = TRUE);
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72
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73
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74 sourcePlate = data.frame();
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75 #for $pmap in $input_data.platemaps
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76
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77 sourcePlate = dplyr::bind_rows(
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78 sourcePlate,
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79 metascreen::importPlateMap(
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80 "$pmap.element_identifier",
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81 .fileFormat = "PlateMap",
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82 galaxy = TRUE,
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83 .sourcePlateConv = $input_data.convert_platemap_format
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84 )
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85 );
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86 #end for
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87
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88 combine_doses = c(1:min(unique(table(listofDoses[,"Drug"]))));
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89 exclude_outer_wells = FALSE;
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90
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91 #if $dispensing_options.well_exclusion.exclude_wells
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92 exclude_outer_wells = $dispensing_options.well_exclusion.outer_wells;
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93 #end if
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94
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95 #if $combination_options.combo_design.type_combination == "all"
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96 #if $combination_options.combo_design.inner_dosing
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97 combine_doses = c(2:(min(unique(table(listofDoses[,"Drug"])))-1));
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98 #end if
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99 #end if
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100
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101 add_untreated = NULL;
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102 #if $dispensing_options.add_untreated.untreated
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103 add_untreated = list(
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104 name = "$dispensing_options.add_untreated.untreated_name",
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105 replicates = $dispensing_options.add_untreated.untreated_replicates);
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106 #end if
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107
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108
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109 listofExWells <-
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110 metascreen::excludeWells(
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111 plateType = $input_data.plateformat,
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112 wells = custom_excluded_wells,
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113 outer.wells = exclude_outer_wells);
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114
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115
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116 listofCombinations <-
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117 metascreen::combineDrugs(
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118 listofDoses,
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119 .combineDoses = combine_doses,
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120 .noReplicates = $combination_options.num_replicates,
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121 .drugRepAttrib = "$combination_options.combo_design.type_combination");
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122
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123
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124 dispensingData <-
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125 metascreen::generateDispensingData(
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126 listofCombinations,
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127 list_of_drugs_raw,
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128 listofDoses,
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129 list_of_volumes_raw,
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130 list_of_controls_raw,
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131 list_of_stock_cons_raw,
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132 sourcePlate,
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133 listofExWells,
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134 .ctrlReplicates = $dispensing_options.num_control_replicates,
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135 .addUntreated = add_untreated,
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136 .finalWellVolume = $dispensing_options.well_volume,
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137 .plateFormat = $input_data.plateformat,
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138 .destinationPlateID = "$dispensing_options.dest_plate_ID",
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139 .randomizeDispensing = $dispensing_options.randomise_dispensing,
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140 .probeDispensing = $dispensing_options.probe_dispensing);
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141
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142 df = as.data.frame(dispensingData[["output"]]);
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143 readr::write_tsv(listofCombinations,file="$doseComb",col_names=T, quote="none");
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144 readr::write_tsv(df,file="$dispensingDF", col_names = T, quote = "none");' 2>&1
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145
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146 ]]></command>
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147 <inputs>
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148
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149 <section name="input_data" title="User-defined input files - see below for strict formatting requirements" expanded="true">
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150 <param name="list_of_doses" type="data" format="txt" label="List of drug doses (CSV)" multiple="false"/>
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151 <param name="list_of_drugs" type="data" format="txt" label="List of drugs (CSV)" multiple="false"/>
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152 <param name="list_of_volumes" type="data" format="txt" label="List of volumes (CSV)" multiple="false"/>
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153 <param name="list_of_ctrls" type="data" format="txt" label="List of controls (CSV)" multiple="false"/>
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154 <param name="list_of_stock_cons" type="data" format="txt" label="List of stock concentrations (CSV)" multiple="false"/>
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155 <param name="platemaps" type="data" format="xml" label="PlateMap file (XML)" multiple="true"/>
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156 <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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157 <param name="plateformat" type="select" label="Plate format" display="radio" multiple="false">
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158 <option value="6">6</option>
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159 <option value="12">12</option>
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160 <option value="24">24</option>
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161 <option value="48">48</option>
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162 <option value="96">96</option>
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163 <option value="384">384</option>
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164 <option value="1536">1536</option>
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165 </param>
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166 </section>
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167
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168 <section name="combination_options" title="Options - drug combination design" expanded="true">
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169 <conditional name="combo_design">
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170 <param name="type_combination" type="select" display="radio" multiple="false" label="Type of dose combinations">
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171 <option value="all">All - both single treatments and combination treatments</option>
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172 <option value="single">Single - only single treatments</option>
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173 </param>
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174 <when value="all">
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175 <param name="inner_dosing" type="boolean" label="Exclude lowest and highest dose (inner dosing only)" truevalue="T" falsevalue="F" checked="false"/>
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176 </when>
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177 </conditional>
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178 <param type="integer" name="num_replicates" label="Number of replicates for each dose combination" value="3" min="1" max="20"/>
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179 </section>
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180 <section name="dispensing_options" title="Options - dispensing layout" expanded="true">
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181 <conditional name="well_exclusion">
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182 <param name="exclude_wells" type="boolean" label="Exclusion of wells" truevalue="T" falsevalue="F" checked="false"/>
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183 <when value="T">
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184 <param name="well_ids" type="text" label="Custom set of well identifiers to exclude (one per line):" area="true"/>
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185 <param name="outer_wells" type="boolean" label="Exclude all outer wells" truevalue="T" falsevalue="F" checked="true"/>
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186 </when>
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187 </conditional>
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188 <param name="num_control_replicates" type="integer" label="Number of control replicates" value="5" min="1" max="10"/>
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189 <param name="well_volume" type="integer" label="Final well volume" value="10" min="1" max="500"/>
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190 <param name="randomise_dispensing" type="boolean" label="Randomise dispensing" truevalue="T" falsevalue="F" checked="true"/>
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191 <param name="probe_dispensing" type="boolean" label="Probe dispensing" truevalue="T" falsevalue="F" checked="false"/>
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192 <param name="dest_plate_ID" type="text" value="PLATE_012" label="A unique destination plate ID - for destination plate barcode"/>
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193 <conditional name="add_untreated">
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194 <param name="untreated" type="boolean" label="Add untreated" truevalue="T" falsevalue="F" checked="true"/>
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195 <when value="T">
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196 <param name="untreated_name" type="text" label="Identifier (name) for untreated" value="Untreated"/>
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197 <param name="untreated_replicates" type="integer" label="Number of untreated replicates" value="5" min="1" max="500"/>
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198 </when>
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199 </conditional>
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200
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201 </section>
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202 </inputs>
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203 <outputs>
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204 <!--data format="xlsx" name="output_xlsx" label="crisprFPA - xlsx"/-->
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205 <data format="txt" name="doseComb" label="doseCombinations - tsv"/>
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206 <data format="txt" name="dispensingDF" label="dispensingData - tsv"/>
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207 </outputs>
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208
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209
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210 <help><![CDATA[
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211 .. class:: infomark
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212
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213 Limitations etc:
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214
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215 -----
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216
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217 **Dataset formats**
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218
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219 The input datasets are in text_ (CSV) format and in XML format. The output datasets are also in text_ formats.
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220
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221 .. _text: ${static_path}/formatHelp.html#text
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222
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223 Specific input file requirements:
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224
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225 - **List of drug doses** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
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226
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227 Provides a list of all the doses for each drug used in
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228 a drug sensitivity screen. The list needs to include a column with the drug number,
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229 drug name, one or multiple columns for the doses, and a column with the unit.
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230 ['Number', 'Drug', '6th Dose', ..., '1st Dose', 'Unit'].
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231 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofdoses.csv
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232
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233 - **List of drugs.** - `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
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234
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235 Provides a list of drugs used in the drug screen. The list
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236 needs to include a column with a unique drug number / id for each drug, the
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237 drug name and the CAS number. ['ID', 'NAME', 'CAS_NUMBER']. For custom
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238 compunds without CAS number, include column, but leave field empty.
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239 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofdrugs.csv
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240
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241 - **List of stock concentrations.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
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242
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243 Provides a list of the stock concentrations
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244 for each drug used in the drug screen. If the stock concentrations are not
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245 known, use the highest dose. The list needs to include column with the unique
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246 drug number / id, the drug name, the stock concentration and the concentration unit.
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247 ['NUMBER', 'NAME', 'CONCENTRATION', 'UNIT'].
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248 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofstockconcentrations.csv
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249
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250 - **List of controls.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
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251
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252 Provides the controls to be used in a drug
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253 screen. The list needs to include a column with the name, CAS number,
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254 dose, unit, the source plate from which the control is dispensed from and the
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255 volume. ['NAME', 'CAS_NUMBER', 'DOSE', 'UNIT', 'SOURCE_PLATE', 'VOLUME'].
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256 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofctrls.csv
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257
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258 - **List of drug volumes.** - A `CSV <https://en.wikipedia.org/wiki/Comma-separated_values/>`_ file
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259
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260 Provides the volumes for each drug that
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261 have been or will be dispensed. The list follows the same format as the
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262 list of drug doses. The list needs to include a column with the drug number,
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263 drug name, one or multiple columns with doses, and a column with the unit.
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264 ['Number', 'Drug', 'Vol 6th Dose', ..., 'Vol 1st Dose', 'Unit'].
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265 An example is shown with https://raw.githubusercontent.com/Enserink-lab/metascreen/main/inst/extdata/library/listofvolumes.csv
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266
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267
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268 - **plateMap** - XML file (s)
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269
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270 One or more plate map files with the contents (usually compounds/drugs) of the
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271 source plate from which drugs are dispensed from. Plate maps can currently be imported
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272 using .PlateMap (XML files) provided by the IncuCyte® Plate Map Editor. **IMPORTANT: when uploading
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273 PlateMap files to Galaxy, please make sure you denote file 'Type' as XML.**
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274
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275 An example is shown with https://github.com/Enserink-lab/metascreen/blob/main/inst/extdata/library/C008.PlateMap
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276
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277 -----
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278
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279 **What it does**
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280
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281 The *pre-experimental* modules of metascreen is intended to serve the following purposes:
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282
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283 allowing to set-up a drug combination screens by (a) generating drug combinations from a list of drugs and
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284 (b) distributing those drug combinations across a number of experimental plates. (c) generating instructions
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285 for dispensing robots for the creation of those experimental plates.
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286
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287
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288
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289
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290
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291
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292 ]]>
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293 </help>
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294
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295 </tool>
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