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planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit a920127294bcfcb708881e28144a77a5c10d46d2-dirty
author | padge |
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date | Wed, 31 Aug 2022 13:17:33 +0000 |
parents | cc0957c46408 |
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<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"> <requirements> <requirement type="package" version="1.7.2">julia</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ## method $t $x $g $r $n_gRNA_total $filename $filename $ϵ_KO --i 10 #if $tools.tool_selector == "gfd" julia '$__tool_directory__/main.jl' gfd $tools.pls $tools.sd $tools.min_gRNA_abundance $tools.max_gRNA_abundance $tools.n_gRNA_total $tools.normalize && mv ./gRNA_reads.xlsx $gRNA_reads #elif $tools.tool_selector == "ged" julia '$__tool_directory__/main.jl' ged $tools.f_act $tools.eps_edit_act $tools.eps_edit_inact $tools.sd_act $tools.n_gRNA_total && mv ./gRNA_edit.xlsx $gRNA_edit #elif $tools.tool_selector == "sim" julia '$__tool_directory__/main.jl' sim $tools.simulation_mode.simulation_mode_selector $tools.n_target_genes $tools.n_designed_gRNAs $tools.simulation_mode.n_gRNA_seqs $tools.n_gRNA_total $tools.p_gRNA_freq $tools.p_gRNA_edit $tools.g_KO --iter $tools.iter #if $tools.simulation_mode.simulation_mode_selector == "4" && mv ./countKOs.xlsx $countKOs #end if #elif $tools.tool_selector == "ccp" julia '$__tool_directory__/main.jl' ccp $tools.bioccp_mode.bioccp_mode_selector $tools.n_target_genes $tools.pls $tools.n_designed_gRNAs $tools.bioccp_mode.n_gRNA_seqs $tools.n_gRNA_total $tools.p_gRNA_freq $tools.p_gRNA_edit $tools.g_KO --step $tools.step --MN $tools.max_pls #end if && mv ./report.html $report ]]></command> <inputs> <conditional name="tools"> <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)"> <option value="gfd">Generate vector with frequencies in the combinatorial gRNA/Cas9 construct library for all gRNAs</option> <option value="ged">Generate vector with genome editing efficiencies for all the gRNAs in the experiment</option> <option value="sim">Simulation-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage</option> <option value="ccp">BioCCP-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage</option> </param> <when value="gfd"> <param name="pls" type="integer" value="75" optional="false" /> <param name="sd" type="integer" value="25" optional="false" /> <param name="min_gRNA_abundance" value="50" type="integer" optional="false" /> <param name="max_gRNA_abundance" value="100" type="integer" optional="false" /> <param name="n_gRNA_total" value="120" type="integer" optional="false" /> <param name="normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="False" label="Convert gRNA abundances into relative frequencies" /> </when> <when value="ged"> <param name="f_act" type="float" value="0.9" optional="false" /> <param name="eps_edit_act" type="float" value="0.95" optional="false" /> <param name="eps_edit_inact" type="float" value="0.1" optional="false" /> <param name="sd_act" type="float" value="0.01" optional="false" /> <param name="n_gRNA_total" type="integer" value="120" optional="false" /> </when> <when value="sim"> <conditional name="simulation_mode"> <param name="simulation_mode_selector" type="select" label="Select simulation mode:"> <option value="1">simulate_Nₓ₁</option> <option value="2">simulate_Nₓ₂</option> <option value="3">simulate_Nₓ₃</option> <option value="4">simulate_Nₓ₂_countKOs</option> </param> <when value="1"> <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="2"> <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="3"> <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="4"> <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> </conditional> <param name="n_target_genes" value="20" label="Number of target genes in the experiment" type="integer" optional="false" /> <param name="n_designed_gRNAs" value="6" label="Number of gRNAs designed per target gene" type="integer" optional="false" /> <param name="n_gRNA_total" value="120" label="Total number of gRNAs in the experiment" type="integer" optional="false" /> <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" /> <param name="p_gRNA_edit" label="Vector (excel file) with genome editing efficiencies for all gRNAs" type="data" format="xlsx" optional="false" /> <param name="g_KO" value="0.8" label="Global knockout efficiency; fraction of mutations leading to effective gene knockout" type="float" optional="false" /> <param name="iter" value="400" label="Number of CRISPR/Cas experiments that are simulated" type="integer" /> </when> <when value="ccp"> <conditional name="bioccp_mode"> <param name="bioccp_mode_selector" type="select" label="Select BioCCP mode:"> <option value="1">BioCCP_Nₓ₁</option> <option value="2">BioCCP_Nₓ₂</option> <option value="3">BioCCP_Nₓ₃</option> <option value="4">BioCCP_Pₓ₁</option> <option value="5">BioCCP_Pₓ₂</option> <option value="6">BioCCP_Pₓ₃</option> <option value="7">BioCCP_γₓ₁</option> <option value="8">BioCCP_γₓ₂</option> <option value="9">BioCCP_γₓ₃</option> </param> <when value="1"> <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="2"> <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="3"> <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="4"> <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="5"> <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="6"> <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="7"> <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="8"> <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> <when value="9"> <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" /> </when> </conditional> <param name="n_target_genes" value="20" label="Number of target genes in the experiment" type="integer" optional="false" /> <param name="n_designed_gRNAs" value="6" label="Number of gRNAs designed per target gene" type="integer" optional="false" /> <param name="n_gRNA_total" value="120" label="Total number of gRNAs in the experiment" type="integer" optional="false" /> <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" /> <param name="p_gRNA_edit" label="Vector (excel file) with genome editing efficiencies for all gRNAs" type="data" format="xlsx" optional="false" /> <param name="g_KO" value="0.8" label="Global knockout efficiency; fraction of mutations leading to effective gene knockout" type="float" optional="false" /> <param name="pls" value="0" label="(Minimum) plant library size" type="integer" optional="true" /> <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" /> <param name="max_pls" value="4000" label="Maximum plant library size (optional for calculating expected combinatorial coverage / plant library size)" type="integer" optional="true" /> </when> </conditional> </inputs> <outputs> <data name="report" format="html" label="report" /> <data name="gRNA_reads" format="xlsx" label="Vector with relative frequencies for all gRNAs in the construct library (normalized!)"> <filter>tools['tool_selector']=='gfd'</filter> </data> <data name="gRNA_edit" format="xlsx" label="Vector with genome editing efficiencies for all gRNAs"> <filter>tools['tool_selector']=='ged'</filter> </data> <data name="countKOs" format="xlsx" label="Vector with counts of the number of knockouts per plant in the experiment" > <filter>tools['tool_selector']=='sim' and tools['bioccp_mode_selector']=='4'</filter> </data> </outputs> <tests> <test> <param name="tool_selector" value="gfd" /> <param name="pls" value="75"/> <param name="sd" value="25" /> <param name="min_gRNA_abundance" value="50" /> <param name="max_gRNA_abundance" value="100" /> <param name="n_gRNA_total" value="120" /> <param name="normalize" value="false" /> <output name="report" file="test_gfd_report.html" compare="sim_size" /> <output name="gRNA_reads" file="test_gRNA_reads.xlsx" ftype="xlsx" compare="sim_size"/> </test> <test> <param name="tool_selector" value="ged" /> <param name="f_act" value="0.9"/> <param name="eps_edit_act" value="0.95" /> <param name="eps_edit_inact" value="0.1" /> <param name="sd_act" value="0.01" /> <param name="n_gRNA_total" value="120" /> <output name="report" file="test_ged_report.html" compare="sim_size" /> <output name="gRNA_edit" file="test_gRNA_edit.xlsx" ftype="xlsx" compare="sim_size"/> </test> <test> <param name="tool_selector" value="sim" /> <param name="simulation_mode_selector" value="4" /> <param name="n_gRNA_seqs" value="2" /> <param name="n_target_genes" value="20" /> <param name="n_designed_gRNAs" value="6" /> <param name="n_gRNA_total" value="120" /> <param name="p_gRNA_freq" value="example_data.xlsx" /> <param name="p_gRNA_edit" value="example_data.xlsx" /> <param name="g_KO" value="0.8" /> <param name="iter" value="10" /> <output name="report" file="test_sim_report.html" compare="sim_size" /> <output name="countKOs" file="test_countKOs.xlsx" ftype="xlsx" compare="sim_size"/> </test> <test> <param name="tool_selector" value="ccp" /> <param name="bioccp_mode_selector" value="9" /> <param name="n_gRNA_seqs" value="3" /> <param name="n_target_genes" value="20" /> <param name="n_designed_gRNAs" value="6" /> <param name="n_gRNA_total" value="120" /> <param name="p_gRNA_freq" value="example_data.xlsx" /> <param name="p_gRNA_edit" value="example_data.xlsx" /> <param name="g_KO" value="0.8" /> <param name="pls" value="0" /> <param name="step" value="5" /> <param name="max_pls" value="4000" /> <output name="report" file="test_ccp_report.html" compare="sim_size" /> </test> </tests> <help><![CDATA[ usage: main.jl [-h] {gfd|ged|sim|ccp} MultiplexCrisprDOE commands: gfd gRNA/Cas9 frequencies ged gRNA/Cas9 editing efficiencies sim simulation-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage (and other relevant statistics) ccp BioCCP-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage (and other relevant statistics) usage: main.jl gfd [--normalize] [--visualize] [--out_file OUT_FILE] [-h] [m] [sd] [l] [u] [n] positional arguments: m plant library size (type: Int64) sd the standard deviation on the gRNA abundances (in terms of absolute or relative frequency) (type: Int64) l minimal gRNA abundance (in terms of absolute or relative frequency) (type: Int64) u maximal gRNA abundance (in terms of absolute or relative frequency) (type: Int64) n the total number of gRNAs in the experiment (type: Int64) optional arguments: --normalize if provided, the gRNA abundances (absolute frequencies) are converted into relative frequencies --visualize if provided, a histogram of all gRNA abundances is plotted --out_file OUT_FILE Output excel file prefix (default: "gRNA_reads") -h, --help show this help message and exit [eps_edit_act] [eps_edit_inact] [sd_act] [n_gRNA_total] positional arguments: f_act fraction of all gRNAs that is active (type: Float16) eps_edit_act Average genome editing efficiency for active gRNAs - mean of the genome editing efficiency distribution for active gRNAs (type: Float16) eps_edit_inact Average genome editing efficiency for inactive gRNAs - mean of the genome editing efficiency distribution for inactive gRNAs (type: Float16) sd_act standard deviation of the genome editing efficiency distributions for active and inactive gRNAs (type: Float16) n_gRNA_total the total number of gRNAs in the experiment (type: Int64) optional arguments: --visualize if provided a histogram of all genome editing efficiency is plotted --out_file OUT_FILE Output excel file prefix (default: "gRNA_edit") -h, --help show this help message and exit usage: main.jl sim [--i I] [-h] [M] [x] [g] [r] [t] [f] [e] [E] positional arguments: M Select simulation mode (1: simulate_Nₓ₁; 2: simulate_Nₓ₂; 3: simulate_Nₓ₃; 4: simulate_Nₓ₂_countKOs) (type: Int64) x number of target genes in the experiment (type: Int64) g number of gRNAs designed per target gene (type: Int64) r number of gRNA sequences per combinatorial gRNA/Cas construct (type: Int64) t total number of gRNAs in the experiment (type: Int64) f vector with relative frequencies for all gRNAs in the construct library (normalized!) e vector with genome editing efficiencies for all gRNAs E global knockout efficiency; fraction of mutations leading to effective gene knockout (type: Float16) optional arguments: --i, --iter I number of CRISPR/Cas experiments that are simulated (type: Int64, default: 500) -h, --help show this help message and exit usage: main.jl ccp [--s S] [--MN MN] [-h] [M] [x] [N] [g] [r] [t] [f] [e] [E] positional arguments: M Select BioCCP mode (1: BioCCP_Nₓ₁; 2: BioCCP_Nₓ₂; 3: BioCCP_Nₓ₃; 4: BioCCP_Pₓ₁; 5: BioCCP_Pₓ₂ ; 6: BioCCP_Pₓ₃; 7: BioCCP_γₓ₁; 8: BioCCP_γₓ₂; 9: BioCCP_γₓ₃) (type: Int64) x number of target genes in the experiment (type: Int64) N (Minimum) plant library size (type: Int64) g number of gRNAs designed per target gene (type: Int64) r number of gRNA sequences per combinatorial gRNA/Cas construct (type: Int64) t total number of gRNAs in the experiment (type: Int64) f File containing vector with relative frequencies for all gRNAs in the construct library (normalized!) e File containing vector with genome editing efficiencies for all gRNAs E global knockout efficiency; fraction of mutations leading to effective gene knockout (type: Float16) optional arguments: --s, --step S Step size for plant library size (optional for calculating expected combinatorial coverage / plant library size) (type: Int64, default: 5) --MN, --max_pl_size MN Maximum plant library size (optional for calculating expected combinatorial coverage / plant library size) (type: Int64, default: 4000) -h, --help show this help message and exit ]]></help> <citations> <citation type="bibtex"> @misc{githubMultiplexCrisprDOE, author = {LastTODO, FirstTODO}, year = {TODO}, title = {MultiplexCrisprDOE}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/kirstvh/MultiplexCrisprDOE}, }</citation> </citations> </tool>