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comparison macros.xml @ 0:c67f0eb6a909 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 16:47:09 +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="0.9.4">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 <yield />
15 <person
16 givenName="Martin"
17 familyName="Čech"
18 url="https://github.com/martenson"
19 identifier="0000-0002-9318-1781" />
20 <person
21 givenName="Jiří"
22 familyName="Novotný"
23 url="https://github.com/xtracko"
24 identifier="0000-0001-5449-3523" />
25 <organization
26 url="https://www.recetox.muni.cz/"
27 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
28 name="RECETOX MUNI"/>
29 </creator>
30 </xml>
31
32 <xml name="inputs">
33 <inputs>
34 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data"
35 help="Mass spectrometry files for peak extraction." />
36 <yield />
37 </inputs>
38 </xml>
39
40 <xml name="history_db">
41 <param name="known_table" type="data" format="parquet" label="known_table"
42 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)." />
43 <section name="history_db" title="Known-Table settings">
44 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
45 help="The ppm tolerance to match identified features to known metabolites/features." />
46 <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"
47 help="The minimum number of occurrences of a historically unseen (unknown) feature to add this feature into the database of known features." />
48 </section>
49 </xml>
50
51 <xml name="noise_filtering">
52 <section name="noise_filtering" title="Noise filtering and peak detection">
53 <yield />
54 <param name="min_pres" type="float" value="0.5"
55 label="min_pres"
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." />
57 <param name="min_run" type="float" value="12"
58 label="min_run"
59 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
60 <param name="mz_tol" type="float" value="1e-05"
61 label="mz_tol"
62 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." />
63 <param name="baseline_correct" type="float" value="0" label="baseline_correct"
64 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." />
65 <param name="baseline_correct_noise_percentile" type="float" value="0.05"
66 label="baseline_correct_noise_percentile"
67 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." />
68 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
69 label="intensity_weighted"
70 help="Whether to weight the local density by signal intensities in initial peak detection." />
71 </section>
72 </xml>
73
74 <xml name="feature_detection">
75 <section name="feature_detection" title="Feature detection">
76 <param name="shape_model" type="select" display="radio"
77 label="shape_model"
78 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.">
79 <option value="Gaussian">Gaussian</option>
80 <option value="bi-Gaussian" selected="true">bi-Gaussian</option>
81 </param>
82 <param name="BIC_factor" type="float" value="2.0"
83 label="BIC_factor"
84 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." />
85 <param name="peak_estim_method" type="select" display="radio"
86 label="peak_estim_method"
87 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
88 <option value="moment" selected="true">Moment</option>
89 <option value="EM">EM</option>
90 </param>
91 <param name="min_bandwidth" type="float" optional="true"
92 label="min_bandwidth (optional)"
93 help="The minimum bandwidth to use in the kernel smoother." />
94 <param name="max_bandwidth" type="float" optional="true"
95 label="max_bandwidth (optional)"
96 help="The maximum bandwidth to use in the kernel smoother." />
97 <param name="sd_cut_min" type="float" value="0.01"
98 label="sd_cut_min"
99 help="The minimum standard deviation of a feature to be not eliminated." />
100 <param name="sd_cut_max" type="float" value="500"
101 label="sd_cut_max"
102 help="The maximum standard deviation of a feature to be not eliminated." />
103 <param name="sigma_ratio_lim_min" type="float" value="0.01"
104 label="sigma_ratio_lim_min"
105 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." />
106 <param name="sigma_ratio_lim_max" type="float" value="100"
107 label="sigma_ratio_lim_max"
108 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." />
109 <param name="component_eliminate" type="float" value="0.01"
110 label="component_eliminate"
111 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." />
112 <param name="moment_power" type="float" value="1"
113 label="moment_power"
114 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
115 </section>
116 </xml>
117
118 <xml name="peak_alignment">
119 <section name="peak_alignment" title="Peak Alignment">
120 <param name="align_chr_tol" type="float" optional="true"
121 label="align_chr_tol (optional)"
122 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." />
123 <param name="align_mz_tol" type="float" optional="true"
124 label="align_mz_tol (optional)"
125 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." />
126 <param name="max_align_mz_diff" type="float" value="0.01"
127 label="max_align_mz_diff"
128 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." />
129 </section>
130 </xml>
131
132 <xml name="weak_signal_recovery">
133 <section name="weak_signal_recovery" title="Weak Signal Recovery">
134 <param name="recover_mz_range" type="float" optional="true"
135 label="recover_mz_range (optional)"
136 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." />
137 <param name="recover_chr_range" type="float" optional="true"
138 label="recover_chr_range (optional)"
139 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." />
140 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
141 label="use_observed_range"
142 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." />
143 <param name="recover_min_count" type="integer" value="3"
144 label="recover_min_count"
145 help="The minimum number of raw data points to be considered as a true feature." />
146 </section>
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>
164 <xml name="output_format">
165 <section name="output_format" title="Output Format">
166 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
167 </section>
168 </xml>
169
170 <xml name="unsupervised_outputs">
171 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
172 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
173 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
174 <yield />
175 </xml>
176
177 <xml name="citations">
178 <citations>
179 <citation type="doi">10.1093/bioinformatics/btp291</citation>
180 <citation type="doi">10.1186/1471-2105-11-559</citation>
181 <citation type="doi">10.1021/pr301053d</citation>
182 <citation type="doi">10.1093/bioinformatics/btu430</citation>
183 <yield />
184 </citations>
185 </xml>
186
187 <token name="@HELP_hybrid@">
188 <![CDATA[
189 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
190 detected features on the same machinery to help detect and quantify lower-intensity peaks.
191
192 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
193 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
194 technique, such as human serum.
195
196 @GENERAL_HELP@
197 ]]>
198 </token>
199
200 <token name="@HELP_unsupervised@">
201 <![CDATA[
202 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
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.
218
219 @GENERAL_HELP@
220 ]]>
221 </token>
222
223 <token name="@GENERAL_HELP@">
224 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
225 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
226 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
227 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
228 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
229 </token>
230 </macros>