Mercurial > repos > recetox > recetox_aplcms_generate_feature_table

comparison macros.xml @ 2:a1f2df6ec4fb draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
author recetox
date Wed, 24 May 2023 14:45:46 +0000
parents e09137c38b4c
children fd078f5746d3
comparison
equal deleted inserted replaced
1:e09137c38b4c 2:a1f2df6ec4fb
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.10.3</token> 2 <token name="@TOOL_VERSION@">0.11.0</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>
91 </when> 91 </when>
92 </conditional> 92 </conditional>
93 </section> 93 </section>
94 </xml> 94 </xml>
95 95
96 <xml name="compute_clusters_params"> 96 <xml name="tolerances">
97 <conditional name="tolerances_input_method"> 97 <param name="mz_tol_relative_ppm" type="float" value="10" label="Relative m/z tolerance [ppm]"
98 <param name="input_method" type="select" display="radio" label="Tolerances input method" 98 help="Relative m/z tolerance to use for grouping features." />
99 help="Tolerances can be entered directly or loaded from a file."> 99 <param name="rt_tol" type="float" value="5" label="Retention time tolerance [unit corresponds to the retention time]"
100 <option value="direct" selected="true">direct</option> 100 help="Retention time tolerance to use for grouping features." />
101 <option value="file">file</option>
102 </param>
103 <when value="direct">
104 <param name="mz_tol_relative" type="float" optional="true" label="Relative m/z tolerance"
105 help="Relative m/z tolerance to use for grouping features.
106 If not provided, it is calculated from the data using kernel density estimation." />
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." />
110 </when>
111 <when value="file">
112 <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet"
113 help="Table containing tolerance values." />
114 </when>
115 </conditional>
116 <param name="mz_tol_absolute" type="float" label="Minimal absolute m/z tolerance [Da]" value="1e-05"
117 help="During the clustering, an m/z tolerance is computed based on the data and the specified relative tolerance.
118 This parameter allows the specification of a minimal value of this tolerance." />
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
122 </xml> 101 </xml>
123 102
124 <xml name="recover_weaker_params"> 103 <xml name="recover_weaker_params">
125 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]" 104 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]"
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. 105 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value.