Mercurial > repos > azomics > autospill
comparison autospill.xml @ 2:3293c160f73c draft default tip
"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/autospill commit 71a5a8cb5b80c7971440a2a1c49a68d311366c6f"
author | azomics |
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date | Tue, 29 Jun 2021 23:53:54 +0000 |
parents | 7f5bf24d5aeb |
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1:7f5bf24d5aeb | 2:3293c160f73c |
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1 <tool id="autospill" name="Autospill" version="0.2.0+galaxy0" profile="19.01" python_template_version="3.5"> | 1 <tool id="autospill" name="Autospill" version="0.2.0+galaxy1" profile="19.01" python_template_version="3.5"> |
2 <description> | 2 <description> |
3 calculates spillover coefficients with robust linear models and then refines spillover coefficients iteratively | 3 calculates spillover coefficients with robust linear models and then refines spillover coefficients iteratively |
4 </description> | 4 </description> |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="0.2.0">r-autospill</requirement> | 6 <requirement type="package" version="0.2.0">r-autospill</requirement> |
113 | 113 |
114 ## triggers generation of a figure with a summary of convergence | 114 ## triggers generation of a figure with a summary of convergence |
115 asp\$figure.convergence.dir <- "figure_convergence" | 115 asp\$figure.convergence.dir <- "figure_convergence" |
116 asp\$table.spillover.dir <- "table_spillover" | 116 asp\$table.spillover.dir <- "table_spillover" |
117 | 117 |
118 #if $remove_forbidden: | |
119 for(c in strsplit('$remove_forbidden', split="")) { | |
120 print(paste0("Removing ",c," from forbidden characters...")) | |
121 asp\$marker.forbidden.char<-gsub(c, "", asp\$marker.forbidden.char) | |
122 } | |
123 #end if | |
124 | |
118 ## Set workers through GALAXY_SLOTS | 125 ## Set workers through GALAXY_SLOTS |
119 asp\$worker.process.n<-args[[3]] | 126 asp\$worker.process.n<-args[[3]] |
120 | 127 |
121 flow.control <- read.flow.control( control.dir, control.def.file, asp ) | 128 flow.control <- read.flow.control( control.dir, control.def.file, asp ) |
122 | 129 |
164 <option value="minimal" selected="true">Minimal - no plot generation</option> | 171 <option value="minimal" selected="true">Minimal - no plot generation</option> |
165 <option value="final.step">Final step - plot generation</option> | 172 <option value="final.step">Final step - plot generation</option> |
166 <option value="paper">Paper</option> | 173 <option value="paper">Paper</option> |
167 <option value="website">Website</option> | 174 <option value="website">Website</option> |
168 </param> --> | 175 </param> --> |
176 <param type="text" name="remove_forbidden" value="" label="Remove characters from autospill's forbidden list of characters" help="Autospill considers all these characters ' !\#$%()*,/:;&?@[\]^{|}~ plus double quotes as forbidden characters. List any of them here to remove them from that list - at a risk of breaking execution." /> | |
169 <param type="boolean" name="get_figure_scatter" label="Get scatter" help="If turned On, the tool will produce scatter plots between setups" checked="true"/> | 177 <param type="boolean" name="get_figure_scatter" label="Get scatter" help="If turned On, the tool will produce scatter plots between setups" checked="true"/> |
170 <param type="boolean" name="get_error" label="Get error matrices/tables" help="If turned On, the tool will produce error matrices for intercepts, coefficients, slope and skewness" checked="false"/> | 178 <param type="boolean" name="get_error" label="Get error matrices/tables" help="If turned On, the tool will produce error matrices for intercepts, coefficients, slope and skewness" checked="false"/> |
171 <param type="boolean" name="get_gates" label="Get gating information" help="If turned On, gating parameters information will be produced" checked="true"/> | 179 <param type="boolean" name="get_gates" label="Get gating information" help="If turned On, gating parameters information will be produced" checked="true"/> |
172 </inputs> | 180 </inputs> |
173 <outputs> | 181 <outputs> |
227 | 235 |
228 **Inputs** | 236 **Inputs** |
229 | 237 |
230 - Collection of control FCS files | 238 - Collection of control FCS files |
231 - Auxiliary control file: Contains metadata for control list. It has to match original names of FCS files uploaded, and those files need to be present in the Collection of control FCS files given. | 239 - Auxiliary control file: Contains metadata for control list. It has to match original names of FCS files uploaded, and those files need to be present in the Collection of control FCS files given. |
232 | 240 - Optional list of characters to remove from autospill's forbidden characters (that otherwise autospill replaces with '-'). |
233 | 241 |
234 **Output** | 242 **Output** |
235 | 243 |
236 - Spillover matrix | 244 - Spillover matrix |
237 - Compensation matrix | 245 - Compensation matrix |