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comparison macros.xml @ 4:69e0da4703b5 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
author recetox
date Fri, 04 Feb 2022 08:31:26 +0000
parents 211cd88b5148
children 10ded21d47c0
comparison
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3:211cd88b5148 4:69e0da4703b5
156 <section name="metadata" title="Optional Metadata" expanded="false"> 156 <section name="metadata" title="Optional Metadata" expanded="false">
157 <param label="metadata" name="batch_order_qc" type="data" format="csv" optional="true" 157 <param label="metadata" name="batch_order_qc" type="data" format="csv" optional="true"
158 help="CSV with sample names (or indices, currently not handled) on rows and columns with: batch 158 help="CSV with sample names (or indices, currently not handled) on rows and columns with: batch
159 number ('batch'), position in sequence ('order') and whether it is a qc sample or not 159 number ('batch'), position in sequence ('order') and whether it is a qc sample or not
160 ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/> 160 ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
161 <!-- <param label="ExpDes" name="ExpDes" type="data" format="RData" optional="true" help=" an R object created by R ExpDes object: data used for record keeping and labelling msp spectral output" /> --> 161 <param label="Experimental design" name="ExpDes" type="data" format="csv" optional="true" help="Definition of experimental design in CSV format." />
162 </section>
163 </xml>
164
165 <xml name="parameters_define_experiment">
166 <section name="define_experiment" title="Define Experiment" expanded="false">
167 <param label="Experiment" name="experiment" type="text" help="Experiment name, no spaces"/>
168 <param label="Species" name="species" type="text" help="Species name"/>
169 <param label="Sample" name="sample" type="text" help="Sample type"/>
170 <param label="Contributor" name="contributor" type="text"
171 help="Individual and/or organizational affiliation"/>
172 <param label="Platform" name="platform" type="select" display="radio" help="Platform">
173 <option value="GC-MS" selected="true">GC-MS</option>
174 <option value="LC-MS">LC-MS</option>
175 </param>
176 </section> 162 </section>
177 </xml> 163 </xml>
178 164
179 <xml name="output_msp"> 165 <xml name="output_msp">
180 <collection label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra" type="list"> 166 <collection label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra" type="list">
222 <![CDATA[ 208 <![CDATA[
223 Documentation 209 Documentation
224 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd 210 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
225 211
226 Upstream Tools 212 Upstream Tools
227 +-------+----------------------+----------------------+------------+ 213 +------------------------------+-------------------------------+----------------------+---------------------+
228 | Name | Output File | Format | Parameter | 214 | Name | Output File | Format | Parameter |
229 +=======+======================+======================+============+ 215 +==============================+===============================+======================+=====================+
230 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj | 216 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj |
231 +-------+----------------------+----------------------+------------+ 217 +------------------------------+-------------------------------+----------------------+---------------------+
218 | RAMClustR define experiment | Table with experiment details | csv | Experimental design |
219 +------------------------------+-------------------------------+----------------------+---------------------+
232 220
233 The tool takes an **xcmsSet** object as input and extracts all relevant information. 221 The tool takes an **xcmsSet** object as input and extracts all relevant information.
234 222
235 +-------+------------------------+--------+------------+ 223 +-------+------------------------+--------+------------+
236 | Name | Output File | Format | Parameter | 224 | Name | Output File | Format | Parameter |
300 features likely to be derived from a single compound. Importantly, this is acheived without looking for 288 features likely to be derived from a single compound. Importantly, this is acheived without looking for
301 specific phenomenon (i.e. sodiation), meaning that grouping can be performed on any dataset, whether it 289 specific phenomenon (i.e. sodiation), meaning that grouping can be performed on any dataset, whether it
302 is poisitive or negative ionization mode, EI or ESI, LC-MS GC-MS or CE-MS, in-source fragment or complex 290 is poisitive or negative ionization mode, EI or ESI, LC-MS GC-MS or CE-MS, in-source fragment or complex
303 adduction event, and predictable or unpredictable signals. 291 adduction event, and predictable or unpredictable signals.
304 </token> 292 </token>
293
294 <token name="@HELP_experiment@">
295 <![CDATA[
296 Create an Experimental Design specification for RAMClustR experiment.
297
298 Downstream Tools
299 +-----------+-----------------------+--------+
300 | Name | Output File | Format |
301 +===========+=======================+========+
302 | RAMClustR | Experiment definition | csv |
303 +-----------+-----------------------+--------+
304
305 ]]>
306 </token>
305 </macros> 307 </macros>