Mercurial > repos > recetox > recetox_aplcms_unsupervised

comparison macros.xml @ 1:4e6281945270 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
author recetox
date Thu, 26 May 2022 16:46:13 +0000
parents d740352d272a
children 10093dea9b3f
comparison
equal deleted inserted replaced
0:d740352d272a 1:4e6281945270
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.9.3</token> 2 <token name="@TOOL_VERSION@">0.9.4</token>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="4.1.0">r-base</requirement> 5 <requirement type="package" version="4.1.0">r-base</requirement>
6 <requirement type="package" version="4.0.1">r-arrow</requirement> 6 <requirement type="package" version="4.0.1">r-arrow</requirement>
7 <requirement type="package" version="0.9.3">r-recetox-aplcms</requirement> 7 <requirement type="package" version="0.9.4">r-recetox-aplcms</requirement>
8 <requirement type="package" version="1.0.7">r-dplyr</requirement> 8 <requirement type="package" version="1.0.7">r-dplyr</requirement>
9 </requirements> 9 </requirements>
10 </xml> 10 </xml>
11 11
12 <xml name="creator"> 12 <xml name="creator">
13 <creator> 13 <creator>
14 <yield />
14 <person 15 <person
15 givenName="Martin" 16 givenName="Martin"
16 familyName="Čech" 17 familyName="Čech"
17 url="https://github.com/martenson" 18 url="https://github.com/martenson"
18 identifier="0000-0002-9318-1781" /> 19 identifier="0000-0002-9318-1781" />
47 </section> 48 </section>
48 </xml> 49 </xml>
49 50
50 <xml name="noise_filtering"> 51 <xml name="noise_filtering">
51 <section name="noise_filtering" title="Noise filtering and peak detection"> 52 <section name="noise_filtering" title="Noise filtering and peak detection">
52 <param name="min_exp" type="integer" min="1" value="2" 53 <yield />
53 label="min_exp"
54 help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." />
55 <param name="min_pres" type="float" value="0.5" 54 <param name="min_pres" type="float" value="0.5"
56 label="min_pres" 55 label="min_pres"
57 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." /> 56 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
58 <param name="min_run" type="float" value="12" 57 <param name="min_run" type="float" value="12"
59 label="min_run" 58 label="min_run"
144 <param name="recover_min_count" type="integer" value="3" 143 <param name="recover_min_count" type="integer" value="3"
145 label="recover_min_count" 144 label="recover_min_count"
146 help="The minimum number of raw data points to be considered as a true feature." /> 145 help="The minimum number of raw data points to be considered as a true feature." />
147 </section> 146 </section>
148 </xml> 147 </xml>
148 <xml name="multibatch_processing">
149 <section name="multibatch_processing" title="Multibatch processing">
150 <param name="min_within_batch_prop_detect" type="float" min="0" max="1" value="0.1"
151 label="minimum_batchwise_prop_detect"
152 help="The minimum detection frequency (relative) of a feature for it to be included in the final feature table." />
153 <param name="min_batch_prop" type="float" min="0" max="1" value="0.5"
154 label="minimum_batch_prop"
155 help="The minimum proportion of batches that must have a given feature. The features that are less abundant than the value won't be reported." />
156 <param name="batch_align_mz_tol" type="float" min="0" value="0.00001"
157 label="batch_align_mz_tol"
158 help="The m/z tolerance level for peak alignment within batch." />
159 <param name="batch_align_chr_tol" type="float" min="0" value="50.0"
160 label="batch_align_chr_tol"
161 help="The retention time tolerance level for peak alignment within batch." />
162 </section>
163 </xml>
149 <xml name="output_format"> 164 <xml name="output_format">
150 <section name="output_format" title="Output Format"> 165 <section name="output_format" title="Output Format">
151 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" /> 166 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
152 </section> 167 </section>
153 </xml> 168 </xml>
154 169
155 <xml name="unsupervised_outputs"> 170 <xml name="unsupervised_outputs">
156 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" /> 171 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
157 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" /> 172 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
158 <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}"> 173 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
159 <discover_datasets pattern="__designation__" directory="corrected" format="parquet" /> 174 <yield />
160 </collection >
161 <collection name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}">
162 <discover_datasets pattern="__designation__" directory="extracted" format="parquet" />
163 </collection >
164 </xml> 175 </xml>
165 176
166 <xml name="citations"> 177 <xml name="citations">
167 <citations> 178 <citations>
168 <citation type="doi">10.1093/bioinformatics/btp291</citation> 179 <citation type="doi">10.1093/bioinformatics/btp291</citation>
169 <citation type="doi">10.1186/1471-2105-11-559</citation> 180 <citation type="doi">10.1186/1471-2105-11-559</citation>
170 <citation type="doi">10.1021/pr301053d</citation> 181 <citation type="doi">10.1021/pr301053d</citation>
171 <citation type="doi">10.1093/bioinformatics/btu430</citation> 182 <citation type="doi">10.1093/bioinformatics/btu430</citation>
183 <yield />
172 </citations> 184 </citations>
173 </xml> 185 </xml>
174 186
175 <token name="@HELP_hybrid@"> 187 <token name="@HELP_hybrid@">
176 <![CDATA[ 188 <![CDATA[
187 199
188 <token name="@HELP_unsupervised@"> 200 <token name="@HELP_unsupervised@">
189 <![CDATA[ 201 <![CDATA[
190 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or 202 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
191 any historically detected features. For such functionality please use the Hybrid version of apLCMS. 203 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
204
205 @GENERAL_HELP@
206 ]]>
207 </token>
208
209 <token name="@HELP_two-step-hybrid@">
210 <![CDATA[
211 This is the **Two-Step Hybrid** version of **apLCMS**. This tool is improved upon the Hybrid version by accounting for the batch
212 effects in multi-batch experiments. As in the Hybrid version, this tool incorporates the knowledge of known metabolites and
213 historically detected features on the same machinery to help detect and quantify lower-intensity peaks.
214
215 **CAUTION**: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
216 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
217 technique, such as human serum.
192 218
193 @GENERAL_HELP@ 219 @GENERAL_HELP@
194 ]]> 220 ]]>
195 </token> 221 </token>
196 222