Mercurial > repos > recetox > ramclustr_define_experiment

comparison macros.xml @ 7:7c50666b88e8 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e
author recetox
date Wed, 17 Apr 2024 07:51:35 +0000
parents 7bbdcce50541
children 87ac0b56b9b0
comparison
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6:bc237895081d 7:7c50666b88e8
182 <param label="Replace zeros" name="replace_zeros" type="boolean" truevalue="TRUE" falsevalue="FALSE" 182 <param label="Replace zeros" name="replace_zeros" type="boolean" truevalue="TRUE" falsevalue="FALSE"
183 checked="true" 183 checked="true"
184 help="NA, NaN, and Inf values are replaced with zero, and zero values are sometimes returned from 184 help="NA, NaN, and Inf values are replaced with zero, and zero values are sometimes returned from
185 peak peaking. When TRUE, zero values will be replaced with a small amount of noise, with noise level 185 peak peaking. When TRUE, zero values will be replaced with a small amount of noise, with noise level
186 set based on the detected signal intensities for that feature."/> 186 set based on the detected signal intensities for that feature."/>
187 <param label="Quality control" name="quality_control" type="boolean" truevalue="TRUE" falsevalue="FALSE"
188 checked="false"
189 help="Add graph to Rplots.pdf output which contains summarize quality control for clustering and for quality
190 control sample variation based on compound ($SpecAbund) and feature ($MSdata and $MSMSdata, if present)."/>
187 <param label="Experimental design metadata" name="ExpDes" type="data" format="csv" optional="true" 191 <param label="Experimental design metadata" name="ExpDes" type="data" format="csv" optional="true"
188 help="Definition of experimental design in CSV format." /> 192 help="Definition of experimental design in CSV format." />
193 </section>
194
195 <section name="filtering" title="Filtering">
196 <conditional name="feature_filter_blanks">
197 <param label="Filter blanks" name="filter_blanks" type="select"
198 help="Is used to remove features which are found at similar intensity in blank samples">
199 <option value="FALSE" selected="true">FALSE</option>
200 <option value="TRUE">TRUE</option>
201 </param>
202 <when value="TRUE">
203 <param label="qc tag" name="qc_tag" type="text" value="QC"
204 help="Character vector of length one or two. If length is two, enter search string and factor name in $phenoData slot
205 (i.e. c('QC', 'sample.type'). If length one (i.e. 'QC'), will search for this string in the 'sample.names' slot by default.
206 Default is 'QC'"/>
207 <param label="blank tag" name="blank_tag" type="text" value="blank"
208 help="See 'qc tag' , but for blanks to use as background. Default is 'blank'"/>
209 <param label="signal to noise (sn)" name="sn" type="integer" value="3"
210 help="Numeric defines the ratio for 'signal'. i.e. sn = 3 indicates that signal intensity must be 3 fold higher in sample than in blanks,
211 on average, to be retained. Default is '3'"/>
212 <param label="Remove blanks" name="remove_blanks" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"
213 help="TRUE by default. This removes any recognized blanks samples from the MSdata and MSMSdata sets after they are used to filter
214 contaminant features."/>
215 </when>
216 <when value="FALSE"></when>
217 </conditional>
218
219 <conditional name="feature_filter_cv">
220 <param label="Filter cv" name="filter_cv" type="select"
221 help="Extractor for xcms objects in preparation for clustering. This function offers normalization
222 by total extracted ion signal. It is recommended to first run 'Filter blanks' to remove non-sample derived signal">
223 <option value="FALSE" selected="true">FALSE</option>
224 <option value="TRUE">TRUE</option>
225 </param>
226 <when value="TRUE">
227 <param label="qc tag" name="qc_tag" type="text" value="QC"
228 help="Character vector of length one or two. If length is two, enter search string and factor name in $phenoData slot
229 (i.e. c('QC', 'sample.type'). If length one (i.e. 'QC'), will search for this string in the 'sample.names' slot by default.
230 Default is 'QC'"/>
231 <param label="Max cv" name="max_cv" type="float" value="0.5" help="Numeric maximum allowable cv for any feature. Default = 0.5."/>
232 </when>
233 <when value="FALSE"></when>
234 </conditional>
189 </section> 235 </section>
190 </xml> 236 </xml>
191 237
192 <xml name="output_msp"> 238 <xml name="output_msp">
193 <collection label="Mass spectra from ${tool.name} on ${on_string} list" name="mass_spectra_collection" type="list"> 239 <collection label="Mass spectra from ${tool.name} on ${on_string} list" name="mass_spectra_collection" type="list">
194 <discover_datasets pattern="__name_and_ext__" directory="spectra" recurse="true" ext="msp"/> 240 <discover_datasets pattern="__name_and_ext__" directory="spectra" recurse="true" ext="msp"/>
195 <filter>not msp_output_details['merge_msp']</filter> 241 <filter>not msp_output_details['merge_msp']</filter>
196 </collection> 242 </collection>
197 <data label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_merged" format="msp"> 243 <data label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_merged" format="msp">
198 <filter>msp_output_details['merge_msp']</filter> 244 <filter>msp_output_details['merge_msp']</filter>
245 </data>
246 <data format="pdf" name="pdf_plot" from_work_dir="Rplots.pdf" label="PDF plot.">
247 <filter>extras['quality_control'] or filtering['feature_filter_cv']['filter_cv'] == "TRUE"</filter>
199 </data> 248 </data>
200 </xml> 249 </xml>
201 250
202 <xml name="citations"> 251 <xml name="citations">
203 <citations> 252 <citations>