Mercurial > repos > padge > mcdoe

comparison mcdoe.xml @ 0:cc0957c46408 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty"
author padge
date Thu, 12 May 2022 17:39:18 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:cc0957c46408
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">
2 <requirements>
3 <requirement type="package" version="1.7.2">julia</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6
7 ## method $t $x $g $r $n_gRNA_total $filename $filename $ϵ_KO --i 10
8
9 #if $tools.tool_selector == "gfd"
10 julia '$__tool_directory__/main.jl' gfd $tools.pls $tools.sd $tools.min_gRNA_abundance
11 $tools.max_gRNA_abundance $tools.n_gRNA_total $tools.normalize
12 &&
13 mv ./gRNA_reads.xlsx $gRNA_reads
14 #elif $tools.tool_selector == "ged"
15 julia '$__tool_directory__/main.jl' ged $tools.f_act $tools.eps_edit_act $tools.eps_edit_inact
16 $tools.sd_act $tools.n_gRNA_total
17 &&
18 mv ./gRNA_edit.xlsx $gRNA_edit
19 #elif $tools.tool_selector == "sim"
20 julia '$__tool_directory__/main.jl' sim $tools.simulation_mode.simulation_mode_selector $tools.n_target_genes
21 $tools.n_designed_gRNAs $tools.simulation_mode.n_gRNA_seqs $tools.n_gRNA_total $tools.p_gRNA_freq
22 $tools.p_gRNA_edit $tools.g_KO --iter $tools.iter
23 #if $tools.simulation_mode.simulation_mode_selector == "4"
24 &&
25 mv ./countKOs.xlsx $countKOs
26 #end if
27 #elif $tools.tool_selector == "ccp"
28 julia '$__tool_directory__/main.jl' ccp $tools.bioccp_mode.bioccp_mode_selector $tools.n_target_genes $tools.pls
29 $tools.n_designed_gRNAs $tools.bioccp_mode.n_gRNA_seqs $tools.n_gRNA_total $tools.p_gRNA_freq
30 $tools.p_gRNA_edit $tools.g_KO --step $tools.step --MN $tools.max_pls
31 #end if
32 &&
33 mv ./report.html $report
34
35 ]]></command>
36 <inputs>
37 <conditional name="tools">
38 <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)">
39 <option value="gfd">Generate vector with frequencies in the combinatorial gRNA/Cas9 construct library for all gRNAs</option>
40 <option value="ged">Generate vector with genome editing efficiencies for all the gRNAs in the experiment</option>
41 <option value="sim">Simulation-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage</option>
42 <option value="ccp">BioCCP-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage</option>
43 </param>
44 <when value="gfd">
45 <param name="pls" type="integer" value="75" optional="false" />
46 <param name="sd" type="integer" value="25" optional="false" />
47 <param name="min_gRNA_abundance" value="50" type="integer" optional="false" />
48 <param name="max_gRNA_abundance" value="100" type="integer" optional="false" />
49 <param name="n_gRNA_total" value="120" type="integer" optional="false" />
50 <param name="normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="False" label="Convert gRNA abundances into relative frequencies" />
51 </when>
52 <when value="ged">
53 <param name="f_act" type="float" value="0.9" optional="false" />
54 <param name="eps_edit_act" type="float" value="0.95" optional="false" />
55 <param name="eps_edit_inact" type="float" value="0.1" optional="false" />
56 <param name="sd_act" type="float" value="0.01" optional="false" />
57 <param name="n_gRNA_total" type="integer" value="120" optional="false" />
58 </when>
59 <when value="sim">
60 <conditional name="simulation_mode">
61 <param name="simulation_mode_selector" type="select" label="Select simulation mode:">
62 <option value="1">simulate_Nₓ₁</option>
63 <option value="2">simulate_Nₓ₂</option>
64 <option value="3">simulate_Nₓ₃</option>
65 <option value="4">simulate_Nₓ₂_countKOs</option>
66 </param>
67 <when value="1">
68 <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
69 </when>
70 <when value="2">
71 <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
72 </when>
73 <when value="3">
74 <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
75 </when>
76 <when value="4">
77 <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
78 </when>
79 </conditional>
80 <param name="n_target_genes" value="20" label="Number of target genes in the experiment" type="integer" optional="false" />
81 <param name="n_designed_gRNAs" value="6" label="Number of gRNAs designed per target gene" type="integer" optional="false" />
82 <param name="n_gRNA_total" value="120" label="Total number of gRNAs in the experiment" type="integer" optional="false" />
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" />
84 <param name="p_gRNA_edit" label="Vector (excel file) with genome editing efficiencies for all gRNAs" type="data" format="xlsx" optional="false" />
85 <param name="g_KO" value="0.8" label="Global knockout efficiency; fraction of mutations leading to effective gene knockout" type="float" optional="false" />
86 <param name="iter" value="400" label="Number of CRISPR/Cas experiments that are simulated" type="integer" />
87 </when>
88 <when value="ccp">
89 <conditional name="bioccp_mode">
90 <param name="bioccp_mode_selector" type="select" label="Select BioCCP mode:">
91 <option value="1">BioCCP_Nₓ₁</option>
92 <option value="2">BioCCP_Nₓ₂</option>
93 <option value="3">BioCCP_Nₓ₃</option>
94 <option value="4">BioCCP_Pₓ₁</option>
95 <option value="5">BioCCP_Pₓ₂</option>
96 <option value="6">BioCCP_Pₓ₃</option>
97 <option value="7">BioCCP_γₓ₁</option>
98 <option value="8">BioCCP_γₓ₂</option>
99 <option value="9">BioCCP_γₓ₃</option>
100 </param>
101 <when value="1">
102 <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
103 </when>
104 <when value="2">
105 <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
106 </when>
107 <when value="3">
108 <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
109 </when>
110 <when value="4">
111 <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
112 </when>
113 <when value="5">
114 <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
115 </when>
116 <when value="6">
117 <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
118 </when>
119 <when value="7">
120 <param name="n_gRNA_seqs" value="1" min="1" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
121 </when>
122 <when value="8">
123 <param name="n_gRNA_seqs" value="2" min="2" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
124 </when>
125 <when value="9">
126 <param name="n_gRNA_seqs" value="3" min="3" label="Number of gRNA sequences per combinatorial gRNA/Cas construct" type="integer" optional="false" />
127 </when>
128 </conditional>
129 <param name="n_target_genes" value="20" label="Number of target genes in the experiment" type="integer" optional="false" />
130 <param name="n_designed_gRNAs" value="6" label="Number of gRNAs designed per target gene" type="integer" optional="false" />
131 <param name="n_gRNA_total" value="120" label="Total number of gRNAs in the experiment" type="integer" optional="false" />
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" />
133 <param name="p_gRNA_edit" label="Vector (excel file) with genome editing efficiencies for all gRNAs" type="data" format="xlsx" optional="false" />
134 <param name="g_KO" value="0.8" label="Global knockout efficiency; fraction of mutations leading to effective gene knockout" type="float" optional="false" />
135 <param name="pls" value="0" label="(Minimum) plant library size" type="integer" optional="true" />
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" />
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" />
138 </when>
139 </conditional>
140 </inputs>
141 <outputs>
142 <data name="report" format="html" label="report" />
143 <data name="gRNA_reads" format="xlsx" label="Vector with relative frequencies for all gRNAs in the construct library (normalized!)">
144 <filter>tools['tool_selector']=='gfd'</filter>
145 </data>
146 <data name="gRNA_edit" format="xlsx" label="Vector with genome editing efficiencies for all gRNAs">
147 <filter>tools['tool_selector']=='ged'</filter>
148 </data>
149 <data name="countKOs" format="xlsx" label="Vector with counts of the number of knockouts per plant in the experiment" >
150 <filter>tools['tool_selector']=='sim' and tools['bioccp_mode_selector']=='4'</filter>
151 </data>
152 </outputs>
153 <tests>
154 <test>
155 <param name="tool_selector" value="gfd" />
156 <param name="pls" value="75"/>
157 <param name="sd" value="25" />
158 <param name="min_gRNA_abundance" value="50" />
159 <param name="max_gRNA_abundance" value="100" />
160 <param name="n_gRNA_total" value="120" />
161 <param name="normalize" value="false" />
162 <output name="report" file="test_gfd_report.html" compare="sim_size" />
163 <output name="gRNA_reads" file="test_gRNA_reads.xlsx" ftype="xlsx" compare="sim_size"/>
164 </test>
165 <test>
166 <param name="tool_selector" value="ged" />
167 <param name="f_act" value="0.9"/>
168 <param name="eps_edit_act" value="0.95" />
169 <param name="eps_edit_inact" value="0.1" />
170 <param name="sd_act" value="0.01" />
171 <param name="n_gRNA_total" value="120" />
172 <output name="report" file="test_ged_report.html" compare="sim_size" />
173 <output name="gRNA_edit" file="test_gRNA_edit.xlsx" ftype="xlsx" compare="sim_size"/>
174 </test>
175 <test>
176 <param name="tool_selector" value="sim" />
177 <param name="simulation_mode_selector" value="4" />
178 <param name="n_gRNA_seqs" value="2" />
179 <param name="n_target_genes" value="20" />
180 <param name="n_designed_gRNAs" value="6" />
181 <param name="n_gRNA_total" value="120" />
182 <param name="p_gRNA_freq" value="example_data.xlsx" />
183 <param name="p_gRNA_edit" value="example_data.xlsx" />
184 <param name="g_KO" value="0.8" />
185 <param name="iter" value="10" />
186 <output name="report" file="test_sim_report.html" compare="sim_size" />
187 <output name="countKOs" file="test_countKOs.xlsx" ftype="xlsx" compare="sim_size"/>
188 </test>
189 <test>
190 <param name="tool_selector" value="ccp" />
191 <param name="bioccp_mode_selector" value="9" />
192 <param name="n_gRNA_seqs" value="3" />
193 <param name="n_target_genes" value="20" />
194 <param name="n_designed_gRNAs" value="6" />
195 <param name="n_gRNA_total" value="120" />
196 <param name="p_gRNA_freq" value="example_data.xlsx" />
197 <param name="p_gRNA_edit" value="example_data.xlsx" />
198 <param name="g_KO" value="0.8" />
199 <param name="pls" value="0" />
200 <param name="step" value="5" />
201 <param name="max_pls" value="4000" />
202 <output name="report" file="test_ccp_report.html" compare="sim_size" />
203 </test>
204 </tests>
205 <help><![CDATA[
206 usage: main.jl [-h] {gfd|ged|sim|ccp}
207
208 MultiplexCrisprDOE
209
210 commands:
211 gfd gRNA/Cas9 frequencies
212 ged gRNA/Cas9 editing efficiencies
213 sim simulation-based approaches for computing the minimal
214 plant library size that guarantees full combinatorial
215 coverage (and other relevant statistics)
216 ccp BioCCP-based approaches for computing the minimal plant
217 library size that guarantees full combinatorial coverage
218 (and other relevant statistics)
219
220 usage: main.jl gfd [--normalize] [--visualize] [--out_file OUT_FILE]
221 [-h] [m] [sd] [l] [u] [n]
222
223 positional arguments:
224 m plant library size (type: Int64)
225 sd the standard deviation on the gRNA abundances
226 (in terms of absolute or relative frequency)
227 (type: Int64)
228 l minimal gRNA abundance (in terms of absolute or
229 relative frequency) (type: Int64)
230 u maximal gRNA abundance (in terms of absolute or
231 relative frequency) (type: Int64)
232 n the total number of gRNAs in the experiment
233 (type: Int64)
234
235 optional arguments:
236 --normalize if provided, the gRNA abundances (absolute
237 frequencies) are converted into relative
238 frequencies
239 --visualize if provided, a histogram of all gRNA abundances
240 is plotted
241 --out_file OUT_FILE Output excel file prefix (default:
242 "gRNA_reads")
243 -h, --help show this help message and exit
244
245 [eps_edit_act] [eps_edit_inact] [sd_act]
246 [n_gRNA_total]
247
248 positional arguments:
249 f_act fraction of all gRNAs that is active (type:
250 Float16)
251 eps_edit_act Average genome editing efficiency for active
252 gRNAs - mean of the genome editing efficiency
253 distribution for active gRNAs (type: Float16)
254 eps_edit_inact Average genome editing efficiency for inactive
255 gRNAs - mean of the genome editing efficiency
256 distribution for inactive gRNAs (type: Float16)
257 sd_act standard deviation of the genome editing
258 efficiency distributions for active and
259 inactive gRNAs (type: Float16)
260 n_gRNA_total the total number of gRNAs in the experiment
261 (type: Int64)
262
263 optional arguments:
264 --visualize if provided a histogram of all genome editing
265 efficiency is plotted
266 --out_file OUT_FILE Output excel file prefix (default: "gRNA_edit")
267 -h, --help show this help message and exit
268
269 usage: main.jl sim [--i I] [-h] [M] [x] [g] [r] [t] [f] [e] [E]
270
271 positional arguments:
272 M Select simulation mode (1: simulate_Nₓ₁; 2:
273 simulate_Nₓ₂; 3: simulate_Nₓ₃; 4:
274 simulate_Nₓ₂_countKOs) (type: Int64)
275 x number of target genes in the experiment (type:
276 Int64)
277 g number of gRNAs designed per target gene (type:
278 Int64)
279 r number of gRNA sequences per combinatorial gRNA/Cas
280 construct (type: Int64)
281 t total number of gRNAs in the experiment (type: Int64)
282 f vector with relative frequencies for all gRNAs in the
283 construct library (normalized!)
284 e vector with genome editing efficiencies for all gRNAs
285 E global knockout efficiency; fraction of mutations
286 leading to effective gene knockout (type: Float16)
287
288 optional arguments:
289 --i, --iter I number of CRISPR/Cas experiments that are simulated
290 (type: Int64, default: 500)
291 -h, --help show this help message and exit
292
293 usage: main.jl ccp [--s S] [--MN MN] [-h] [M] [x] [N] [g] [r] [t] [f]
294 [e] [E]
295
296 positional arguments:
297 M Select BioCCP mode (1: BioCCP_Nₓ₁; 2:
298 BioCCP_Nₓ₂; 3: BioCCP_Nₓ₃; 4: BioCCP_Pₓ₁; 5:
299 BioCCP_Pₓ₂ ; 6: BioCCP_Pₓ₃; 7: BioCCP_γₓ₁; 8:
300 BioCCP_γₓ₂; 9: BioCCP_γₓ₃) (type: Int64)
301 x number of target genes in the experiment
302 (type: Int64)
303 N (Minimum) plant library size (type: Int64)
304 g number of gRNAs designed per target gene
305 (type: Int64)
306 r number of gRNA sequences per combinatorial
307 gRNA/Cas construct (type: Int64)
308 t total number of gRNAs in the experiment (type:
309 Int64)
310 f File containing vector with relative
311 frequencies for all gRNAs in the construct
312 library (normalized!)
313 e File containing vector with genome editing
314 efficiencies for all gRNAs
315 E global knockout efficiency; fraction of
316 mutations leading to effective gene knockout
317 (type: Float16)
318
319 optional arguments:
320 --s, --step S Step size for plant library size (optional for
321 calculating expected combinatorial coverage /
322 plant library size) (type: Int64, default: 5)
323 --MN, --max_pl_size MN
324 Maximum plant library size (optional for
325 calculating expected combinatorial coverage /
326 plant library size) (type: Int64, default:
327 4000)
328 -h, --help show this help message and exit
329 ]]></help>
330 <citations>
331 <citation type="bibtex">
332 @misc{githubMultiplexCrisprDOE,
333 author = {LastTODO, FirstTODO},
334 year = {TODO},
335 title = {MultiplexCrisprDOE},
336 publisher = {GitHub},
337 journal = {GitHub repository},
338 url = {https://github.com/kirstvh/MultiplexCrisprDOE},
339 }</citation>
340 </citations>
341 </tool>