Mercurial > repos > recetox > recetox_aplcms_compute_clusters

comparison macros.xml @ 1:092bbb03a217 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
author recetox
date Mon, 03 Apr 2023 14:56:58 +0000
parents 82737757f3d5
children ce00e1d03c31
comparison
equal deleted inserted replaced
0:82737757f3d5 1:092bbb03a217
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.10.1</token> 2 <token name="@TOOL_VERSION@">0.10.3</token>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement> 5 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
6 <requirement type="package" version="2.5.2">pymzml</requirement> 6 <requirement type="package" version="2.5.2">pymzml</requirement>
7 </requirements> 7 </requirements>
40 name="RECETOX MUNI"/> 40 name="RECETOX MUNI"/>
41 </creator> 41 </creator>
42 </xml> 42 </xml>
43 43
44 <xml name="remove_noise_params"> 44 <xml name="remove_noise_params">
45 <param name="min_pres" type="float" value="0.5" label="min_pres" 45 <param name="min_pres" type="float" value="0.5" label="Minimal signal presence [fraction of scans]"
46 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." /> 46 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
47 <param name="min_run" type="float" value="12" label="min_run" 47 <param name="min_run" type="float" value="12" label="Minimal elution time [unit corresponds to the retention time]"
48 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." /> 48 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
49 <param name="mz_tol" type="float" value="1e-05" label="mz_tol" 49 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]"
50 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." /> 50 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value.
51 <param name="baseline_correct" type="float" value="0" label="baseline_correct" 51 This value, multiplied by the m/z value, becomes the cutoff level.
52 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." /> 52 The recommended value is the machine's nominal accuracy level (e.g. for FTMS, it is 10)." />
53 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="intensity_weighted" 53 <param name="baseline_correct" type="float" value="0" label="Baseline correction [unit of signal intensity]"
54 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." />
55 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Weight intensity"
54 help="Whether to weight the local density by signal intensities in initial peak detection." /> 56 help="Whether to weight the local density by signal intensities in initial peak detection." />
55 </xml> 57 </xml>
56 58
57 <xml name="generate_feature_table_params"> 59 <xml name="generate_feature_table_params">
58 <param name="sd_cut_min" type="float" value="0.01" label="sd_cut_min" 60 <param name="BIC_factor" type="float" value="2.0" label="BIC factor"
59 help="The minimum standard deviation of a feature to be not eliminated." /> 61 help="A factor influencing Bayesian information criterion (BIC) in estimation of RT peak shape.
60 <param name="sd_cut_max" type="float" value="500" label="sd_cut_max" 62 If the value is larger than 1, models with more peaks are penalized more." />
61 help="The maximum standard deviation of a feature to be not eliminated." /> 63 <section name="advanced" title="Advanced" expanded="false">
62 <conditional name="shape"> 64 <param name="component_eliminate" type="float" value="0.01" label="Component eliminate"
63 <param name="shape_model" type="select" display="radio" label="shape_model" 65 help="In fitting mixture of bi-Gaussian model of an EIC, when a component accounts for a proportion of intensities less than this value, the component will be ignored." />
64 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."> 66 <section name="shape_model" title="Shape model deviations" expanded="true">
65 <option value="Gaussian">Gaussian</option> 67 <param name="sigma_ratio_lim_min" type="float" optional="true" label="Minimal sigma ratio"
66 <option value="bi-Gaussian" selected="true">bi-Gaussian</option> 68 help="The lower limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." />
67 </param> 69 <param name="sigma_ratio_lim_max" type="float" optional="true" label="Maximal sigma ratio"
68 <when value="bi-Gaussian"> 70 help="The upper limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." />
69 <param name="sigma_ratio_lim_min" type="float" value="0.01" label="sigma_ratio_lim_min" 71 </section>
70 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." /> 72 <conditional name="sd_cut">
71 <param name="sigma_ratio_lim_max" type="float" value="100" label="sigma_ratio_lim_max" 73 <param name="sd_cut_bounds" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Standard deviations boundaries."
72 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." /> 74 help="Do not apply any limitations on the standard deviations." />
73 </when> 75 <when value="FALSE">
74 </conditional> 76 <param name="sd_cut_min" type="float" value="0.01" label="Minimal standard deviation"
75 <param name="peak_estim_method" type="select" display="radio" label="peak_estim_method" 77 help="The minimum standard deviation - features with a standard deviation lower than this number are eliminated." />
76 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM."> 78 <param name="sd_cut_max" type="float" value="500" label="Maximal standard deviation"
77 <option value="moment" selected="true">Moment</option> 79 help="The maximum standard deviation - features with a standard deviation greater than this number are eliminated." />
78 <option value="EM">EM</option> 80 </when>
79 </param> 81 </conditional>
80 <param name="moment_power" type="float" value="1" label="moment_power" 82 <conditional name="peak_estim">
81 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." /> 83 <param name="peak_estim_method" type="select" display="radio" label="Peak estimation method"
82 <param name="component_eliminate" type="float" value="0.01" label="component_eliminate" 84 help="The estimation method for parameters of the bi-Gaussian peak model. Two possible algorithms: moment and EM (expectation maximization).">
83 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." /> 85 <option value="moment">Moment</option>
84 <param name="BIC_factor" type="float" value="2.0" label="BIC_factor" 86 <option value="EM" selected="true">EM</option>
85 help="A factor influencing Bayesian information criterion (BIC) in estimation of RT peak shape. If the value is larger than 1, models with more peaks are penalized more." /> 87 </param>
88 <when value="moment">
89 <param name="moment_power" type="float" value="1" label="Moment power"
90 help="The power parameter for data transformation when fitting the bi-Gaussian mixture model in an EIC." />
91 </when>
92 </conditional>
93 </section>
86 </xml> 94 </xml>
87 95
88 <xml name="compute_clusters_params"> 96 <xml name="compute_clusters_params">
89 <conditional name="tolerances_input_method"> 97 <conditional name="tolerances_input_method">
90 <param name="input_method" type="select" display="radio" label="Tolerances input method" 98 <param name="input_method" type="select" display="radio" label="Tolerances input method"
91 help="Tolerances can be entered directly or loaded from a file."> 99 help="Tolerances can be entered directly or loaded from a file.">
92 <option value="direct" selected="true">direct</option> 100 <option value="direct" selected="true">direct</option>
93 <option value="file">file</option> 101 <option value="file">file</option>
94 </param> 102 </param>
95 <when value="direct"> 103 <when value="direct">
96 <param name="mz_tol_relative" type="float" optional="true" label="mz_tol_relative" 104 <param name="mz_tol_relative" type="float" optional="true" label="Relative m/z tolerance"
97 help="Relative m/z tolerance to use for grouping features." /> 105 help="Relative m/z tolerance to use for grouping features.
98 <param name="rt_tol_relative" type="float" optional="true" label="rt_tol_relative" 106 If not provided, it is calculated from the data using kernel density estimation." />
99 help="Relative retention time tolerance to use for grouping features." /> 107 <param name="rt_tol_relative" type="float" optional="true" label="Relative rt tolerance [unit corresponds to the retention time]"
108 help="Relative retention time tolerance to use for grouping features.
109 If not provided, it is calculated from the data using kernel density estimation." />
100 </when> 110 </when>
101 <when value="file"> 111 <when value="file">
102 <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet" 112 <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet"
103 help="Table containing tolerance values." /> 113 help="Table containing tolerance values." />
104 </when> 114 </when>
105 </conditional> 115 </conditional>
106 <param name="mz_tol_absolute" type="float" label="mz_tol_absolute" value="1e-05" 116 <param name="mz_tol_absolute" type="float" label="Minimal absolute m/z tolerance [Da]" value="1e-05"
107 help="Absolute m/z tolerance to use for grouping features." /> 117 help="During the clustering, an m/z tolerance is computed based on the data and the specified relative tolerance.
108 <param name="mz_max_diff" type="float" label="mz_max_diff" value="0.01" 118 This parameter allows the specification of a minimal value of this tolerance." />
109 help="Maximum difference between feature m/z values to belong to the same cluster." /> 119 <param name="mz_max_diff" type="float" label="Maximal m/z difference [Da]" value="0.01"
120 help="Maximum allowed difference between feature m/z values to belong to the same cluster." />
121
110 </xml> 122 </xml>
111 123
112 <xml name="recover_weaker_params"> 124 <xml name="recover_weaker_params">
113 <param name="mz_tol" type="float" value="1e-05" label="mz_tol" 125 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]"
114 help="The m/z tolerance level for the grouping of data points. This value is expressed as the 126 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value.
115 fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. 127 This value, multiplied by the m/z value, becomes the cutoff level.
116 The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. 128 The recommended value is the machine's nominal accuracy level (e.g. for FTMS, it is 10)." />
117 For FTMS, 1e-5 is recommended." /> 129 <param name="recover_mz_range" type="float" optional="true" label="Range for m/z recovery [ppm]"
118 <param name="recover_mz_range" type="float" optional="true" label="recover_mz_range" 130
119 help="The m/z around the feature m/z to search for observations. The default value is NA, in which 131 help="The m/z around the feature m/z to search for observations. If not given, 1.5 times the m/z tolerance
120 case 1.5 times the m/z tolerance in the aligned object will be used." /> 132 in the aligned object will be used." />
121 <param name="recover_rt_range" type="float" optional="true" label="recover_rt_range" 133 <param name="recover_rt_range" type="float" optional="true" label="Range for rt recovery [unit of retention time]"
122 help="The retention time around the feature retention time to search for observations. 134 help="The retention time around the feature retention time to search for observations.
123 The default value is NA, in which case 0.5 times the retention time tolerance in the aligned 135 If not given, 0.5 times the retention time tolerance in the aligned object will be used." />
124 object will be used." />
125 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" 136 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
126 label="use_observed_range" help="If the value is true, the actual range of the observed locations of 137 label="Use observed rt range" help="Use the minimal and maximal rt values per feature." />
127 the feature in all the spectra will be used." /> 138 <param name="recover_min_count" type="integer" value="3" label="Minimal count to recover"
128 <param name="recover_min_count" type="integer" value="3" label="recover_min_count"
129 help="The minimum number of raw data points to be considered as a true feature." /> 139 help="The minimum number of raw data points to be considered as a true feature." />
130 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" 140 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
131 label="intensity_weighted" help="Whether to weight the local density by signal intensities in initial peak detection." /> 141 label="Weight intensity" help="Whether to weight the local density by signal intensities in initial peak detection." />
132 </xml> 142 </xml>
133 143
134 <xml name="bandwidth_params"> 144 <xml name="bandwidth_params">
135 <param name="bandwidth" type="float" value="0.5" label="bandwidth" 145 <param name="bandwidth" type="float" value="0.5" label="Bandwidth factor" min="0" max="1"
136 help="A value between zero and one. Multiplying this value to the length of the signal along 146 help="Parameter used to scale down the overall range of retention times (the bandwidth) assumed in the kernel smoother
137 the time axis helps determine the bandwidth in the kernel smoother used for peak identification." /> 147 used for peak identification. The value is between zero and one. The minimal and maximal bandwidth can be limited by explicit values." />
138 <param name="min_bandwidth" type="float" optional="true" label="min_bandwidth" 148 <param name="min_bandwidth" type="float" optional="true" label="Minimal bandwidth [unit corresponds to the retention time]"
139 help="The minimum bandwidth to use in the kernel smoother." /> 149 help="The lower limit on the resulting bandwidth. If not given, it is estimated based on the overall range of retention times in the profile." />
140 <param name="max_bandwidth" type="float" optional="true" label="max_bandwidth" 150 <param name="max_bandwidth" type="float" optional="true" label="Maximal bandwidth [unit corresponds to the retention time]"
141 help="The maximum bandwidth to use in the kernel smoother." /> 151 help="The upper limit on the resulting bandwidth. If not given, it is estimated based on the overall range of retention times in the profile" />
152
142 </xml> 153 </xml>
143 154
144 <xml name="citations"> 155 <xml name="citations">
145 <citations> 156 <citations>
146 <citation type="doi">10.1093/bioinformatics/btp291</citation> 157 <citation type="doi">10.1093/bioinformatics/btp291</citation>