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
date Tue, 29 Jun 2021 23:53:54 +0000
parents 7f5bf24d5aeb
children
comparison
equal deleted inserted replaced
1:7f5bf24d5aeb 2:3293c160f73c
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 ' !\#$%()*,/:;&amp;?@[\]^{|}~ 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