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annotate mcdoe.xml @ 0:cc0957c46408 draft

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"planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty"
author padge
date Thu, 12 May 2022 17:39:18 +0000
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cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty"
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1 <tool id="mcdoe" name="MultiplexCrisprDOE - simulation- and BioCCP-based approaches for computing the minimal plant library size" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="1.7.2">julia</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6
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7 ## method $t $x $g $r $n_gRNA_total $filename $filename $ϵ_KO --i 10
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8
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9 #if $tools.tool_selector == "gfd"
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10 julia '$__tool_directory__/main.jl' gfd $tools.pls $tools.sd $tools.min_gRNA_abundance
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11 $tools.max_gRNA_abundance $tools.n_gRNA_total $tools.normalize
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12 &&
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13 mv ./gRNA_reads.xlsx $gRNA_reads
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14 #elif $tools.tool_selector == "ged"
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15 julia '$__tool_directory__/main.jl' ged $tools.f_act $tools.eps_edit_act $tools.eps_edit_inact
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16 $tools.sd_act $tools.n_gRNA_total
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17 &&
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18 mv ./gRNA_edit.xlsx $gRNA_edit
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19 #elif $tools.tool_selector == "sim"
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20 julia '$__tool_directory__/main.jl' sim $tools.simulation_mode.simulation_mode_selector $tools.n_target_genes
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21 $tools.n_designed_gRNAs $tools.simulation_mode.n_gRNA_seqs $tools.n_gRNA_total $tools.p_gRNA_freq
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22 $tools.p_gRNA_edit $tools.g_KO --iter $tools.iter
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23 #if $tools.simulation_mode.simulation_mode_selector == "4"
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24 &&
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25 mv ./countKOs.xlsx $countKOs
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26 #end if
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27 #elif $tools.tool_selector == "ccp"
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28 julia '$__tool_directory__/main.jl' ccp $tools.bioccp_mode.bioccp_mode_selector $tools.n_target_genes $tools.pls
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29 $tools.n_designed_gRNAs $tools.bioccp_mode.n_gRNA_seqs $tools.n_gRNA_total $tools.p_gRNA_freq
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30 $tools.p_gRNA_edit $tools.g_KO --step $tools.step --MN $tools.max_pls
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31 #end if
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32 &&
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33 mv ./report.html $report
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34
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35 ]]></command>
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36 <inputs>
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37 <conditional name="tools">
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38 <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)">
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39 <option value="gfd">Generate vector with frequencies in the combinatorial gRNA/Cas9 construct library for all gRNAs</option>
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40 <option value="ged">Generate vector with genome editing efficiencies for all the gRNAs in the experiment</option>
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41 <option value="sim">Simulation-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage</option>
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42 <option value="ccp">BioCCP-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage</option>
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43 </param>
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44 <when value="gfd">
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45 <param name="pls" type="integer" value="75" optional="false" />
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46 <param name="sd" type="integer" value="25" optional="false" />
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47 <param name="min_gRNA_abundance" value="50" type="integer" optional="false" />
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48 <param name="max_gRNA_abundance" value="100" type="integer" optional="false" />
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49 <param name="n_gRNA_total" value="120" type="integer" optional="false" />
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50 <param name="normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="False" label="Convert gRNA abundances into relative frequencies" />
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51 </when>
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52 <when value="ged">
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53 <param name="f_act" type="float" value="0.9" optional="false" />
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54 <param name="eps_edit_act" type="float" value="0.95" optional="false" />
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55 <param name="eps_edit_inact" type="float" value="0.1" optional="false" />
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56 <param name="sd_act" type="float" value="0.01" optional="false" />
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57 <param name="n_gRNA_total" type="integer" value="120" optional="false" />
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58 </when>
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59 <when value="sim">
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60 <conditional name="simulation_mode">
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61 <param name="simulation_mode_selector" type="select" label="Select simulation mode:">
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62 <option value="1">simulate_Nₓ₁</option>
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63 <option value="2">simulate_Nₓ₂</option>
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64 <option value="3">simulate_Nₓ₃</option>
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65 <option value="4">simulate_Nₓ₂_countKOs</option>
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66 </param>
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67 <when value="1">
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68 <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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69 </when>
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70 <when value="2">
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71 <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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72 </when>
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73 <when value="3">
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74 <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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75 </when>
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76 <when value="4">
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77 <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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78 </when>
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79 </conditional>
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80 <param name="n_target_genes" value="20" label="Number of target genes in the experiment" type="integer" optional="false" />
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81 <param name="n_designed_gRNAs" value="6" label="Number of gRNAs designed per target gene" type="integer" optional="false" />
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82 <param name="n_gRNA_total" value="120" label="Total number of gRNAs in the experiment" type="integer" optional="false" />
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83 <param name="p_gRNA_freq" label="Vector (excel file) with relative frequencies for all gRNAs in the construct library (normalized!)" type="data" format="xlsx" optional="false" />
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84 <param name="p_gRNA_edit" label="Vector (excel file) with genome editing efficiencies for all gRNAs" type="data" format="xlsx" optional="false" />
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85 <param name="g_KO" value="0.8" label="Global knockout efficiency; fraction of mutations leading to effective gene knockout" type="float" optional="false" />
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86 <param name="iter" value="400" label="Number of CRISPR/Cas experiments that are simulated" type="integer" />
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87 </when>
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88 <when value="ccp">
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89 <conditional name="bioccp_mode">
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90 <param name="bioccp_mode_selector" type="select" label="Select BioCCP mode:">
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91 <option value="1">BioCCP_Nₓ₁</option>
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92 <option value="2">BioCCP_Nₓ₂</option>
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93 <option value="3">BioCCP_Nₓ₃</option>
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94 <option value="4">BioCCP_Pₓ₁</option>
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95 <option value="5">BioCCP_Pₓ₂</option>
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96 <option value="6">BioCCP_Pₓ₃</option>
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97 <option value="7">BioCCP_γₓ₁</option>
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98 <option value="8">BioCCP_γₓ₂</option>
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99 <option value="9">BioCCP_γₓ₃</option>
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100 </param>
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101 <when value="1">
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102 <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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103 </when>
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104 <when value="2">
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105 <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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106 </when>
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107 <when value="3">
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108 <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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109 </when>
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110 <when value="4">
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111 <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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112 </when>
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113 <when value="5">
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114 <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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115 </when>
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116 <when value="6">
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117 <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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118 </when>
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119 <when value="7">
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120 <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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121 </when>
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122 <when value="8">
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123 <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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124 </when>
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125 <when value="9">
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126 <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
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127 </when>
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128 </conditional>
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129 <param name="n_target_genes" value="20" label="Number of target genes in the experiment" type="integer" optional="false" />
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130 <param name="n_designed_gRNAs" value="6" label="Number of gRNAs designed per target gene" type="integer" optional="false" />
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131 <param name="n_gRNA_total" value="120" label="Total number of gRNAs in the experiment" type="integer" optional="false" />
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132 <param name="p_gRNA_freq" label="Vector (excel file) with relative frequencies for all gRNAs in the construct library (normalized!)" type="data" format="xlsx" optional="false" />
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133 <param name="p_gRNA_edit" label="Vector (excel file) with genome editing efficiencies for all gRNAs" type="data" format="xlsx" optional="false" />
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134 <param name="g_KO" value="0.8" label="Global knockout efficiency; fraction of mutations leading to effective gene knockout" type="float" optional="false" />
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135 <param name="pls" value="0" label="(Minimum) plant library size" type="integer" optional="true" />
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136 <param name="step" value="5" label="Step size for plant library size (optional for calculating expected combinatorial coverage / plant library size)" type="integer" optional="true" />
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137 <param name="max_pls" value="4000" label="Maximum plant library size (optional for calculating expected combinatorial coverage / plant library size)" type="integer" optional="true" />
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138 </when>
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139 </conditional>
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140 </inputs>
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141 <outputs>
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142 <data name="report" format="html" label="report" />
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143 <data name="gRNA_reads" format="xlsx" label="Vector with relative frequencies for all gRNAs in the construct library (normalized!)">
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144 <filter>tools['tool_selector']=='gfd'</filter>
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145 </data>
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146 <data name="gRNA_edit" format="xlsx" label="Vector with genome editing efficiencies for all gRNAs">
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147 <filter>tools['tool_selector']=='ged'</filter>
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148 </data>
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149 <data name="countKOs" format="xlsx" label="Vector with counts of the number of knockouts per plant in the experiment" >
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150 <filter>tools['tool_selector']=='sim' and tools['bioccp_mode_selector']=='4'</filter>
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151 </data>
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152 </outputs>
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153 <tests>
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154 <test>
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155 <param name="tool_selector" value="gfd" />
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156 <param name="pls" value="75"/>
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157 <param name="sd" value="25" />
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158 <param name="min_gRNA_abundance" value="50" />
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159 <param name="max_gRNA_abundance" value="100" />
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160 <param name="n_gRNA_total" value="120" />
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161 <param name="normalize" value="false" />
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162 <output name="report" file="test_gfd_report.html" compare="sim_size" />
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163 <output name="gRNA_reads" file="test_gRNA_reads.xlsx" ftype="xlsx" compare="sim_size"/>
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164 </test>
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165 <test>
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166 <param name="tool_selector" value="ged" />
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167 <param name="f_act" value="0.9"/>
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168 <param name="eps_edit_act" value="0.95" />
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169 <param name="eps_edit_inact" value="0.1" />
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170 <param name="sd_act" value="0.01" />
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171 <param name="n_gRNA_total" value="120" />
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172 <output name="report" file="test_ged_report.html" compare="sim_size" />
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173 <output name="gRNA_edit" file="test_gRNA_edit.xlsx" ftype="xlsx" compare="sim_size"/>
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174 </test>
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175 <test>
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176 <param name="tool_selector" value="sim" />
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177 <param name="simulation_mode_selector" value="4" />
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178 <param name="n_gRNA_seqs" value="2" />
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179 <param name="n_target_genes" value="20" />
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180 <param name="n_designed_gRNAs" value="6" />
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181 <param name="n_gRNA_total" value="120" />
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182 <param name="p_gRNA_freq" value="example_data.xlsx" />
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183 <param name="p_gRNA_edit" value="example_data.xlsx" />
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184 <param name="g_KO" value="0.8" />
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185 <param name="iter" value="10" />
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186 <output name="report" file="test_sim_report.html" compare="sim_size" />
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187 <output name="countKOs" file="test_countKOs.xlsx" ftype="xlsx" compare="sim_size"/>
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188 </test>
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189 <test>
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190 <param name="tool_selector" value="ccp" />
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191 <param name="bioccp_mode_selector" value="9" />
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192 <param name="n_gRNA_seqs" value="3" />
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193 <param name="n_target_genes" value="20" />
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194 <param name="n_designed_gRNAs" value="6" />
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195 <param name="n_gRNA_total" value="120" />
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196 <param name="p_gRNA_freq" value="example_data.xlsx" />
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197 <param name="p_gRNA_edit" value="example_data.xlsx" />
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198 <param name="g_KO" value="0.8" />
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199 <param name="pls" value="0" />
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200 <param name="step" value="5" />
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201 <param name="max_pls" value="4000" />
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202 <output name="report" file="test_ccp_report.html" compare="sim_size" />
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203 </test>
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204 </tests>
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205 <help><![CDATA[
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206 usage: main.jl [-h] {gfd|ged|sim|ccp}
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207
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208 MultiplexCrisprDOE
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209
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210 commands:
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211 gfd gRNA/Cas9 frequencies
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212 ged gRNA/Cas9 editing efficiencies
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213 sim simulation-based approaches for computing the minimal
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214 plant library size that guarantees full combinatorial
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215 coverage (and other relevant statistics)
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216 ccp BioCCP-based approaches for computing the minimal plant
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217 library size that guarantees full combinatorial coverage
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218 (and other relevant statistics)
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219
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220 usage: main.jl gfd [--normalize] [--visualize] [--out_file OUT_FILE]
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221 [-h] [m] [sd] [l] [u] [n]
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222
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223 positional arguments:
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224 m plant library size (type: Int64)
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225 sd the standard deviation on the gRNA abundances
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226 (in terms of absolute or relative frequency)
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227 (type: Int64)
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228 l minimal gRNA abundance (in terms of absolute or
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229 relative frequency) (type: Int64)
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230 u maximal gRNA abundance (in terms of absolute or
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231 relative frequency) (type: Int64)
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232 n the total number of gRNAs in the experiment
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233 (type: Int64)
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234
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235 optional arguments:
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236 --normalize if provided, the gRNA abundances (absolute
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237 frequencies) are converted into relative
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238 frequencies
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239 --visualize if provided, a histogram of all gRNA abundances
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240 is plotted
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241 --out_file OUT_FILE Output excel file prefix (default:
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242 "gRNA_reads")
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243 -h, --help show this help message and exit
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244
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245 [eps_edit_act] [eps_edit_inact] [sd_act]
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246 [n_gRNA_total]
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247
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248 positional arguments:
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249 f_act fraction of all gRNAs that is active (type:
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250 Float16)
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251 eps_edit_act Average genome editing efficiency for active
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252 gRNAs - mean of the genome editing efficiency
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253 distribution for active gRNAs (type: Float16)
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254 eps_edit_inact Average genome editing efficiency for inactive
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255 gRNAs - mean of the genome editing efficiency
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256 distribution for inactive gRNAs (type: Float16)
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257 sd_act standard deviation of the genome editing
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258 efficiency distributions for active and
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259 inactive gRNAs (type: Float16)
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260 n_gRNA_total the total number of gRNAs in the experiment
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261 (type: Int64)
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262
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263 optional arguments:
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264 --visualize if provided a histogram of all genome editing
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265 efficiency is plotted
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266 --out_file OUT_FILE Output excel file prefix (default: "gRNA_edit")
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267 -h, --help show this help message and exit
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268
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269 usage: main.jl sim [--i I] [-h] [M] [x] [g] [r] [t] [f] [e] [E]
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270
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271 positional arguments:
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272 M Select simulation mode (1: simulate_Nₓ₁; 2:
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273 simulate_Nₓ₂; 3: simulate_Nₓ₃; 4:
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274 simulate_Nₓ₂_countKOs) (type: Int64)
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275 x number of target genes in the experiment (type:
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276 Int64)
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277 g number of gRNAs designed per target gene (type:
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278 Int64)
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279 r number of gRNA sequences per combinatorial gRNA/Cas
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280 construct (type: Int64)
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281 t total number of gRNAs in the experiment (type: Int64)
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282 f vector with relative frequencies for all gRNAs in the
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283 construct library (normalized!)
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284 e vector with genome editing efficiencies for all gRNAs
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285 E global knockout efficiency; fraction of mutations
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286 leading to effective gene knockout (type: Float16)
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287
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288 optional arguments:
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289 --i, --iter I number of CRISPR/Cas experiments that are simulated
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290 (type: Int64, default: 500)
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291 -h, --help show this help message and exit
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292
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293 usage: main.jl ccp [--s S] [--MN MN] [-h] [M] [x] [N] [g] [r] [t] [f]
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294 [e] [E]
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295
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296 positional arguments:
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297 M Select BioCCP mode (1: BioCCP_Nₓ₁; 2:
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298 BioCCP_Nₓ₂; 3: BioCCP_Nₓ₃; 4: BioCCP_Pₓ₁; 5:
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299 BioCCP_Pₓ₂ ; 6: BioCCP_Pₓ₃; 7: BioCCP_γₓ₁; 8:
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300 BioCCP_γₓ₂; 9: BioCCP_γₓ₃) (type: Int64)
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301 x number of target genes in the experiment
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302 (type: Int64)
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303 N (Minimum) plant library size (type: Int64)
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304 g number of gRNAs designed per target gene
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305 (type: Int64)
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306 r number of gRNA sequences per combinatorial
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307 gRNA/Cas construct (type: Int64)
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308 t total number of gRNAs in the experiment (type:
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309 Int64)
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310 f File containing vector with relative
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311 frequencies for all gRNAs in the construct
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312 library (normalized!)
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313 e File containing vector with genome editing
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314 efficiencies for all gRNAs
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315 E global knockout efficiency; fraction of
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316 mutations leading to effective gene knockout
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317 (type: Float16)
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318
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319 optional arguments:
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320 --s, --step S Step size for plant library size (optional for
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321 calculating expected combinatorial coverage /
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322 plant library size) (type: Int64, default: 5)
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323 --MN, --max_pl_size MN
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324 Maximum plant library size (optional for
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325 calculating expected combinatorial coverage /
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326 plant library size) (type: Int64, default:
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327 4000)
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328 -h, --help show this help message and exit
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329 ]]></help>
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330 <citations>
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331 <citation type="bibtex">
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332 @misc{githubMultiplexCrisprDOE,
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333 author = {LastTODO, FirstTODO},
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334 year = {TODO},
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335 title = {MultiplexCrisprDOE},
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336 publisher = {GitHub},
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337 journal = {GitHub repository},
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338 url = {https://github.com/kirstvh/MultiplexCrisprDOE},
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339 }</citation>
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340 </citations>
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341 </tool>