Mercurial > repos > recetox > recetox_aplcms_align_features

comparison macros.xml @ 0:57c644d3f24c draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author recetox
date Fri, 10 Jun 2022 10:17:46 +0000
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1 <macros>
2 <token name="@TOOL_VERSION@">0.9.4</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="4.1.0">r-base</requirement>
6 <requirement type="package" version="4.0.1">r-arrow</requirement>
7 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
8 <requirement type="package" version="1.0.7">r-dplyr</requirement>
9 </requirements>
10 </xml>
11
12 <xml name="creator">
13 <creator>
14 <person
15 givenName="Maksym"
16 familyName="Skoryk"
17 url="https://github.com/maximskorik"
18 identifier="0000-0003-2056-8018" />
19 <person
20 givenName="Matej"
21 familyName="Troják"
22 url="https://github.com/xtrojak"
23 identifier="0000-0003-0841-2707" />
24 <person
25 givenName="Martin"
26 familyName="Čech"
27 url="https://github.com/martenson"
28 identifier="0000-0002-9318-1781" />
29 <person
30 givenName="Jiří"
31 familyName="Novotný"
32 url="https://github.com/xtracko"
33 identifier="0000-0001-5449-3523" />
34 <organization
35 url="https://www.recetox.muni.cz/"
36 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
37 name="RECETOX MUNI"/>
38 </creator>
39 </xml>
40
41 <xml name="inputs">
42 <inputs>
43 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data"
44 help="Mass spectrometry files for peak extraction." />
45 <yield />
46 </inputs>
47 </xml>
48
49 <xml name="history_db">
50 <param name="known_table" type="data" format="parquet" label="known_table"
51 help="A data table containing the known metabolite ions and previously found features. The table must contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional), neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed m/z value of previously found features), Number_profiles_processed (the total number of processed samples to build this database), Percent_found (the percentage of historically processed samples in which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value), RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." />
52 <section name="history_db" title="Known-Table settings">
53 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
54 help="The ppm tolerance to match identified features to known metabolites/features." />
55 <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"
56 help="The minimum number of occurrences of a historically unseen (unknown) feature to add this feature into the database of known features." />
57 </section>
58 </xml>
59
60 <xml name="noise_filtering">
61 <section name="noise_filtering" title="Noise filtering and peak detection">
62 <yield />
63 <param name="min_pres" type="float" value="0.5"
64 label="min_pres"
65 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
66 <param name="min_run" type="float" value="12"
67 label="min_run"
68 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
69 <param name="mz_tol" type="float" value="1e-05"
70 label="mz_tol"
71 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. For FTMS, 1e-5 is recommended." />
72 <param name="baseline_correct" type="float" value="0" label="baseline_correct"
73 help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted. The default value is NA, in which case the program uses a percentile of the height of the noise groups. If given a value, the value will be used as the threshold, and baseline.correct.noise.percentile will be ignored." />
74 <param name="baseline_correct_noise_percentile" type="float" value="0.05"
75 label="baseline_correct_noise_percentile"
76 help="The percentile of signal strength of those EIC that don't pass the run filter, to be used as the baseline threshold of signal strength." />
77 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
78 label="intensity_weighted"
79 help="Whether to weight the local density by signal intensities in initial peak detection." />
80 </section>
81 </xml>
82
83 <xml name="feature_detection">
84 <section name="feature_detection" title="Feature detection">
85 <param name="shape_model" type="select" display="radio"
86 label="shape_model"
87 help="The mathematical model for the shape of a peak. There are two choices - bi-Gaussian and Gaussian. When the peaks are asymmetric, the bi-Gaussian is better.">
88 <option value="Gaussian">Gaussian</option>
89 <option value="bi-Gaussian" selected="true">bi-Gaussian</option>
90 </param>
91 <param name="BIC_factor" type="float" value="2.0"
92 label="BIC_factor"
93 help="The factor that is multiplied on the number of parameters to modify the BIC criterion. If larger than 1, models with more peaks are penalized more." />
94 <param name="peak_estim_method" type="select" display="radio"
95 label="peak_estim_method"
96 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
97 <option value="moment" selected="true">Moment</option>
98 <option value="EM">EM</option>
99 </param>
100 <param name="min_bandwidth" type="float" optional="true"
101 label="min_bandwidth (optional)"
102 help="The minimum bandwidth to use in the kernel smoother." />
103 <param name="max_bandwidth" type="float" optional="true"
104 label="max_bandwidth (optional)"
105 help="The maximum bandwidth to use in the kernel smoother." />
106 <param name="sd_cut_min" type="float" value="0.01"
107 label="sd_cut_min"
108 help="The minimum standard deviation of a feature to be not eliminated." />
109 <param name="sd_cut_max" type="float" value="500"
110 label="sd_cut_max"
111 help="The maximum standard deviation of a feature to be not eliminated." />
112 <param name="sigma_ratio_lim_min" type="float" value="0.01"
113 label="sigma_ratio_lim_min"
114 help="The lower limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." />
115 <param name="sigma_ratio_lim_max" type="float" value="100"
116 label="sigma_ratio_lim_max"
117 help="The upper limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." />
118 <param name="component_eliminate" type="float" value="0.01"
119 label="component_eliminate"
120 help="In fitting mixture of bi-Gaussian (or Gaussian) model of an EIC, when a component accounts for a proportion of intensities less than this value, the component will be ignored." />
121 <param name="moment_power" type="float" value="1"
122 label="moment_power"
123 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
124 </section>
125 </xml>
126
127 <xml name="peak_alignment">
128 <section name="peak_alignment" title="Peak Alignment">
129 <param name="align_chr_tol" type="float" optional="true"
130 label="align_chr_tol (optional)"
131 help="The retention time tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data." />
132 <param name="align_mz_tol" type="float" optional="true"
133 label="align_mz_tol (optional)"
134 help="The m/z tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data. The tolerance is given in absolute numbers, not scaled, i.e. for 10ppm tolerance enter '1e-05'. This value, multiplied by the m/z value, becomes the cutoff level." />
135 <param name="max_align_mz_diff" type="float" value="0.01"
136 label="max_align_mz_diff"
137 help="As the m/z tolerance is expressed in relative terms (ppm), it may not be suitable when the m/z range is wide. This parameter limits the tolerance in absolute terms. It mostly influences feature matching in higher m/z range." />
138 </section>
139 </xml>
140
141 <xml name="weak_signal_recovery">
142 <section name="weak_signal_recovery" title="Weak Signal Recovery">
143 <param name="recover_mz_range" type="float" optional="true"
144 label="recover_mz_range (optional)"
145 help="The m/z around the feature m/z to search for observations. The default value is NA, in which case 1.5 times the m/z tolerance in the aligned object will be used." />
146 <param name="recover_chr_range" type="float" optional="true"
147 label="recover_chr_range (optional)"
148 help="The retention time around the feature retention time to search for observations. The default value is NA, in which case 0.5 times the retention time tolerance in the aligned object will be used." />
149 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
150 label="use_observed_range"
151 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." />
152 <param name="recover_min_count" type="integer" value="3"
153 label="recover_min_count"
154 help="The minimum number of raw data points to be considered as a true feature." />
155 </section>
156 </xml>
157 <xml name="multibatch_processing">
158 <section name="multibatch_processing" title="Multibatch processing">
159 <param name="min_within_batch_prop_detect" type="float" min="0" max="1" value="0.1"
160 label="minimum_batchwise_prop_detect"
161 help="The minimum detection frequency (relative) of a feature for it to be included in the final feature table." />
162 <param name="min_batch_prop" type="float" min="0" max="1" value="0.5"
163 label="minimum_batch_prop"
164 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." />
165 <param name="batch_align_mz_tol" type="float" min="0" value="0.00001"
166 label="batch_align_mz_tol"
167 help="The m/z tolerance level for peak alignment within batch." />
168 <param name="batch_align_chr_tol" type="float" min="0" value="50.0"
169 label="batch_align_chr_tol"
170 help="The retention time tolerance level for peak alignment within batch." />
171 </section>
172 </xml>
173
174 <xml name="mz_tol_macro">
175 <param name="mz_tol" type="float" value="1e-05" label="mz_tol"
176 help="The m/z tolerance level for the grouping of data points. This value is expressed as the
177 fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level.
178 The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6.
179 For FTMS, 1e-5 is recommended." />
180 </xml>
181
182 <xml name="output_format">
183 <section name="output_format" title="Output Format">
184 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
185 </section>
186 </xml>
187
188 <xml name="unsupervised_outputs">
189 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
190 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
191 <yield />
192 </xml>
193
194 <xml name="citations">
195 <citations>
196 <citation type="doi">10.1093/bioinformatics/btp291</citation>
197 <citation type="doi">10.1186/1471-2105-11-559</citation>
198 <citation type="doi">10.1021/pr301053d</citation>
199 <citation type="doi">10.1093/bioinformatics/btu430</citation>
200 <yield />
201 </citations>
202 </xml>
203
204 <token name="@HELP_hybrid@">
205 <![CDATA[
206 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
207 detected features on the same machinery to help detect and quantify lower-intensity peaks.
208
209 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
210 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
211 technique, such as human serum.
212
213 @GENERAL_HELP@
214 ]]>
215 </token>
216
217 <token name="@HELP_unsupervised@">
218 <![CDATA[
219 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
220 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
221
222 @GENERAL_HELP@
223 ]]>
224 </token>
225
226 <token name="@HELP_two-step-hybrid@">
227 <![CDATA[
228 This is the **Two-Step Hybrid** version of **apLCMS**. This tool is improved upon the Hybrid version by accounting for the batch
229 effects in multi-batch experiments. As in the Hybrid version, this tool incorporates the knowledge of known metabolites and
230 historically detected features on the same machinery to help detect and quantify lower-intensity peaks.
231
232 **CAUTION**: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
233 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
234 technique, such as human serum.
235
236 @GENERAL_HELP@
237 ]]>
238 </token>
239
240 <token name="@GENERAL_HELP@">
241 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
242 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
243 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
244 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
245 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
246 </token>
247 </macros>